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45 #include "gromacs/gmxpreprocess/toputil.h"
46 #include "gromacs/legacyheaders/chargegroup.h"
47 #include "gromacs/legacyheaders/inputrec.h"
48 #include "gromacs/legacyheaders/macros.h"
49 #include "gromacs/legacyheaders/names.h"
50 #include "gromacs/legacyheaders/network.h"
51 #include "gromacs/legacyheaders/readinp.h"
52 #include "gromacs/legacyheaders/typedefs.h"
53 #include "gromacs/legacyheaders/warninp.h"
54 #include "gromacs/math/units.h"
55 #include "gromacs/math/vec.h"
56 #include "gromacs/mdlib/calc_verletbuf.h"
57 #include "gromacs/pbcutil/pbc.h"
58 #include "gromacs/topology/block.h"
59 #include "gromacs/topology/index.h"
60 #include "gromacs/topology/mtop_util.h"
61 #include "gromacs/topology/symtab.h"
62 #include "gromacs/utility/cstringutil.h"
63 #include "gromacs/utility/fatalerror.h"
64 #include "gromacs/utility/smalloc.h"
69 /* Resource parameters
70 * Do not change any of these until you read the instruction
71 * in readinp.h. Some cpp's do not take spaces after the backslash
72 * (like the c-shell), which will give you a very weird compiler
76 typedef struct t_inputrec_strings
78 char tcgrps[STRLEN], tau_t[STRLEN], ref_t[STRLEN],
79 acc[STRLEN], accgrps[STRLEN], freeze[STRLEN], frdim[STRLEN],
80 energy[STRLEN], user1[STRLEN], user2[STRLEN], vcm[STRLEN], x_compressed_groups[STRLEN],
81 couple_moltype[STRLEN], orirefitgrp[STRLEN], egptable[STRLEN], egpexcl[STRLEN],
82 wall_atomtype[STRLEN], wall_density[STRLEN], deform[STRLEN], QMMM[STRLEN],
84 char fep_lambda[efptNR][STRLEN];
85 char lambda_weights[STRLEN];
88 char anneal[STRLEN], anneal_npoints[STRLEN],
89 anneal_time[STRLEN], anneal_temp[STRLEN];
90 char QMmethod[STRLEN], QMbasis[STRLEN], QMcharge[STRLEN], QMmult[STRLEN],
91 bSH[STRLEN], CASorbitals[STRLEN], CASelectrons[STRLEN], SAon[STRLEN],
92 SAoff[STRLEN], SAsteps[STRLEN], bTS[STRLEN], bOPT[STRLEN];
93 char efield_x[STRLEN], efield_xt[STRLEN], efield_y[STRLEN],
94 efield_yt[STRLEN], efield_z[STRLEN], efield_zt[STRLEN];
96 } gmx_inputrec_strings;
98 static gmx_inputrec_strings *is = NULL;
100 void init_inputrec_strings()
104 gmx_incons("Attempted to call init_inputrec_strings before calling done_inputrec_strings. Only one inputrec (i.e. .mdp file) can be parsed at a time.");
109 void done_inputrec_strings()
115 static char swapgrp[STRLEN], splitgrp0[STRLEN], splitgrp1[STRLEN], solgrp[STRLEN];
118 egrptpALL, /* All particles have to be a member of a group. */
119 egrptpALL_GENREST, /* A rest group with name is generated for particles *
120 * that are not part of any group. */
121 egrptpPART, /* As egrptpALL_GENREST, but no name is generated *
122 * for the rest group. */
123 egrptpONE /* Merge all selected groups into one group, *
124 * make a rest group for the remaining particles. */
127 static const char *constraints[eshNR+1] = {
128 "none", "h-bonds", "all-bonds", "h-angles", "all-angles", NULL
131 static const char *couple_lam[ecouplamNR+1] = {
132 "vdw-q", "vdw", "q", "none", NULL
135 void init_ir(t_inputrec *ir, t_gromppopts *opts)
137 snew(opts->include, STRLEN);
138 snew(opts->define, STRLEN);
139 snew(ir->fepvals, 1);
140 snew(ir->expandedvals, 1);
141 snew(ir->simtempvals, 1);
144 static void GetSimTemps(int ntemps, t_simtemp *simtemp, double *temperature_lambdas)
149 for (i = 0; i < ntemps; i++)
151 /* simple linear scaling -- allows more control */
152 if (simtemp->eSimTempScale == esimtempLINEAR)
154 simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*temperature_lambdas[i];
156 else if (simtemp->eSimTempScale == esimtempGEOMETRIC) /* should give roughly equal acceptance for constant heat capacity . . . */
158 simtemp->temperatures[i] = simtemp->simtemp_low * pow(simtemp->simtemp_high/simtemp->simtemp_low, (1.0*i)/(ntemps-1));
160 else if (simtemp->eSimTempScale == esimtempEXPONENTIAL)
162 simtemp->temperatures[i] = simtemp->simtemp_low + (simtemp->simtemp_high-simtemp->simtemp_low)*(gmx_expm1(temperature_lambdas[i])/gmx_expm1(1.0));
167 sprintf(errorstr, "eSimTempScale=%d not defined", simtemp->eSimTempScale);
168 gmx_fatal(FARGS, errorstr);
175 static void _low_check(gmx_bool b, char *s, warninp_t wi)
179 warning_error(wi, s);
183 static void check_nst(const char *desc_nst, int nst,
184 const char *desc_p, int *p,
189 if (*p > 0 && *p % nst != 0)
191 /* Round up to the next multiple of nst */
192 *p = ((*p)/nst + 1)*nst;
193 sprintf(buf, "%s should be a multiple of %s, changing %s to %d\n",
194 desc_p, desc_nst, desc_p, *p);
199 static gmx_bool ir_NVE(const t_inputrec *ir)
201 return ((ir->eI == eiMD || EI_VV(ir->eI)) && ir->etc == etcNO);
204 static int lcd(int n1, int n2)
209 for (i = 2; (i <= n1 && i <= n2); i++)
211 if (n1 % i == 0 && n2 % i == 0)
220 static void process_interaction_modifier(const t_inputrec *ir, int *eintmod)
222 if (*eintmod == eintmodPOTSHIFT_VERLET)
224 if (ir->cutoff_scheme == ecutsVERLET)
226 *eintmod = eintmodPOTSHIFT;
230 *eintmod = eintmodNONE;
235 void check_ir(const char *mdparin, t_inputrec *ir, t_gromppopts *opts,
237 /* Check internal consistency.
238 * NOTE: index groups are not set here yet, don't check things
239 * like temperature coupling group options here, but in triple_check
242 /* Strange macro: first one fills the err_buf, and then one can check
243 * the condition, which will print the message and increase the error
246 #define CHECK(b) _low_check(b, err_buf, wi)
247 char err_buf[256], warn_buf[STRLEN];
253 t_lambda *fep = ir->fepvals;
254 t_expanded *expand = ir->expandedvals;
256 set_warning_line(wi, mdparin, -1);
258 /* BASIC CUT-OFF STUFF */
259 if (ir->rcoulomb < 0)
261 warning_error(wi, "rcoulomb should be >= 0");
265 warning_error(wi, "rvdw should be >= 0");
268 !(ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0))
270 warning_error(wi, "rlist should be >= 0");
272 sprintf(err_buf, "nstlist can not be smaller than 0. (If you were trying to use the heuristic neighbour-list update scheme for efficient buffering for improved energy conservation, please use the Verlet cut-off scheme instead.)");
273 CHECK(ir->nstlist < 0);
275 process_interaction_modifier(ir, &ir->coulomb_modifier);
276 process_interaction_modifier(ir, &ir->vdw_modifier);
278 if (ir->cutoff_scheme == ecutsGROUP)
281 "The group cutoff scheme is deprecated since GROMACS 5.0 and will be removed in a future "
282 "release when all interaction forms are supported for the verlet scheme. The verlet "
283 "scheme already scales better, and it is compatible with GPUs and other accelerators.");
285 /* BASIC CUT-OFF STUFF */
286 if (ir->rlist == 0 ||
287 !((ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > ir->rlist) ||
288 (ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > ir->rlist)))
290 /* No switched potential and/or no twin-range:
291 * we can set the long-range cut-off to the maximum of the other cut-offs.
293 ir->rlistlong = max_cutoff(ir->rlist, max_cutoff(ir->rvdw, ir->rcoulomb));
295 else if (ir->rlistlong < 0)
297 ir->rlistlong = max_cutoff(ir->rlist, max_cutoff(ir->rvdw, ir->rcoulomb));
298 sprintf(warn_buf, "rlistlong was not set, setting it to %g (no buffer)",
300 warning(wi, warn_buf);
302 if (ir->rlistlong == 0 && ir->ePBC != epbcNONE)
304 warning_error(wi, "Can not have an infinite cut-off with PBC");
306 if (ir->rlistlong > 0 && (ir->rlist == 0 || ir->rlistlong < ir->rlist))
308 warning_error(wi, "rlistlong can not be shorter than rlist");
310 if (IR_TWINRANGE(*ir) && ir->nstlist == 0)
312 warning_error(wi, "Can not have nstlist == 0 with twin-range interactions");
316 if (ir->rlistlong == ir->rlist)
320 else if (ir->rlistlong > ir->rlist && ir->nstcalclr == 0)
322 warning_error(wi, "With different cutoffs for electrostatics and VdW, nstcalclr must be -1 or a positive number");
325 if (ir->cutoff_scheme == ecutsVERLET)
329 /* Normal Verlet type neighbor-list, currently only limited feature support */
330 if (inputrec2nboundeddim(ir) < 3)
332 warning_error(wi, "With Verlet lists only full pbc or pbc=xy with walls is supported");
334 if (ir->rcoulomb != ir->rvdw)
336 warning_error(wi, "With Verlet lists rcoulomb!=rvdw is not supported");
338 if (ir->vdwtype == evdwSHIFT || ir->vdwtype == evdwSWITCH)
340 if (ir->vdw_modifier == eintmodNONE ||
341 ir->vdw_modifier == eintmodPOTSHIFT)
343 ir->vdw_modifier = (ir->vdwtype == evdwSHIFT ? eintmodFORCESWITCH : eintmodPOTSWITCH);
345 sprintf(warn_buf, "Replacing vdwtype=%s by the equivalent combination of vdwtype=%s and vdw_modifier=%s", evdw_names[ir->vdwtype], evdw_names[evdwCUT], eintmod_names[ir->vdw_modifier]);
346 warning_note(wi, warn_buf);
348 ir->vdwtype = evdwCUT;
352 sprintf(warn_buf, "Unsupported combination of vdwtype=%s and vdw_modifier=%s", evdw_names[ir->vdwtype], eintmod_names[ir->vdw_modifier]);
353 warning_error(wi, warn_buf);
357 if (!(ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME))
359 warning_error(wi, "With Verlet lists only cut-off and PME LJ interactions are supported");
361 if (!(ir->coulombtype == eelCUT ||
362 (EEL_RF(ir->coulombtype) && ir->coulombtype != eelRF_NEC) ||
363 EEL_PME(ir->coulombtype) || ir->coulombtype == eelEWALD))
365 warning_error(wi, "With Verlet lists only cut-off, reaction-field, PME and Ewald electrostatics are supported");
367 if (!(ir->coulomb_modifier == eintmodNONE ||
368 ir->coulomb_modifier == eintmodPOTSHIFT))
370 sprintf(warn_buf, "coulomb_modifier=%s is not supported with the Verlet cut-off scheme", eintmod_names[ir->coulomb_modifier]);
371 warning_error(wi, warn_buf);
374 if (ir->implicit_solvent != eisNO)
376 warning_error(wi, "Implicit solvent is not (yet) supported with the with Verlet lists.");
379 if (ir->nstlist <= 0)
381 warning_error(wi, "With Verlet lists nstlist should be larger than 0");
384 if (ir->nstlist < 10)
386 warning_note(wi, "With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note that with the Verlet scheme, nstlist has no effect on the accuracy of your simulation.");
389 rc_max = max(ir->rvdw, ir->rcoulomb);
391 if (ir->verletbuf_tol <= 0)
393 if (ir->verletbuf_tol == 0)
395 warning_error(wi, "Can not have Verlet buffer tolerance of exactly 0");
398 if (ir->rlist < rc_max)
400 warning_error(wi, "With verlet lists rlist can not be smaller than rvdw or rcoulomb");
403 if (ir->rlist == rc_max && ir->nstlist > 1)
405 warning_note(wi, "rlist is equal to rvdw and/or rcoulomb: there is no explicit Verlet buffer. The cluster pair list does have a buffering effect, but choosing a larger rlist might be necessary for good energy conservation.");
410 if (ir->rlist > rc_max)
412 warning_note(wi, "You have set rlist larger than the interaction cut-off, but you also have verlet-buffer-tolerance > 0. Will set rlist using verlet-buffer-tolerance.");
415 if (ir->nstlist == 1)
417 /* No buffer required */
422 if (EI_DYNAMICS(ir->eI))
424 if (inputrec2nboundeddim(ir) < 3)
426 warning_error(wi, "The box volume is required for calculating rlist from the energy drift with verlet-buffer-tolerance > 0. You are using at least one unbounded dimension, so no volume can be computed. Either use a finite box, or set rlist yourself together with verlet-buffer-tolerance = -1.");
428 /* Set rlist temporarily so we can continue processing */
433 /* Set the buffer to 5% of the cut-off */
434 ir->rlist = (1.0 + verlet_buffer_ratio_nodynamics)*rc_max;
439 /* No twin-range calculations with Verlet lists */
440 ir->rlistlong = ir->rlist;
443 if (ir->nstcalclr == -1)
445 /* if rlist=rlistlong, this will later be changed to nstcalclr=0 */
446 ir->nstcalclr = ir->nstlist;
448 else if (ir->nstcalclr > 0)
450 if (ir->nstlist > 0 && (ir->nstlist % ir->nstcalclr != 0))
452 warning_error(wi, "nstlist must be evenly divisible by nstcalclr. Use nstcalclr = -1 to automatically follow nstlist");
455 else if (ir->nstcalclr < -1)
457 warning_error(wi, "nstcalclr must be a positive number (divisor of nstcalclr), or -1 to follow nstlist.");
460 if (EEL_PME(ir->coulombtype) && ir->rcoulomb > ir->rlist && ir->nstcalclr > 1)
462 warning_error(wi, "When used with PME, the long-range component of twin-range interactions must be updated every step (nstcalclr)");
465 /* GENERAL INTEGRATOR STUFF */
466 if (!(ir->eI == eiMD || EI_VV(ir->eI)))
470 if (ir->eI == eiVVAK)
472 sprintf(warn_buf, "Integrator method %s is implemented primarily for validation purposes; for molecular dynamics, you should probably be using %s or %s", ei_names[eiVVAK], ei_names[eiMD], ei_names[eiVV]);
473 warning_note(wi, warn_buf);
475 if (!EI_DYNAMICS(ir->eI))
479 if (EI_DYNAMICS(ir->eI))
481 if (ir->nstcalcenergy < 0)
483 ir->nstcalcenergy = ir_optimal_nstcalcenergy(ir);
484 if (ir->nstenergy != 0 && ir->nstenergy < ir->nstcalcenergy)
486 /* nstcalcenergy larger than nstener does not make sense.
487 * We ideally want nstcalcenergy=nstener.
491 ir->nstcalcenergy = lcd(ir->nstenergy, ir->nstlist);
495 ir->nstcalcenergy = ir->nstenergy;
499 else if ( (ir->nstenergy > 0 && ir->nstcalcenergy > ir->nstenergy) ||
500 (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
501 (ir->nstcalcenergy > ir->fepvals->nstdhdl) ) )
504 const char *nsten = "nstenergy";
505 const char *nstdh = "nstdhdl";
506 const char *min_name = nsten;
507 int min_nst = ir->nstenergy;
509 /* find the smallest of ( nstenergy, nstdhdl ) */
510 if (ir->efep != efepNO && ir->fepvals->nstdhdl > 0 &&
511 (ir->nstenergy == 0 || ir->fepvals->nstdhdl < ir->nstenergy))
513 min_nst = ir->fepvals->nstdhdl;
516 /* If the user sets nstenergy small, we should respect that */
518 "Setting nstcalcenergy (%d) equal to %s (%d)",
519 ir->nstcalcenergy, min_name, min_nst);
520 warning_note(wi, warn_buf);
521 ir->nstcalcenergy = min_nst;
524 if (ir->epc != epcNO)
526 if (ir->nstpcouple < 0)
528 ir->nstpcouple = ir_optimal_nstpcouple(ir);
531 if (IR_TWINRANGE(*ir))
533 check_nst("nstlist", ir->nstlist,
534 "nstcalcenergy", &ir->nstcalcenergy, wi);
535 if (ir->epc != epcNO)
537 check_nst("nstlist", ir->nstlist,
538 "nstpcouple", &ir->nstpcouple, wi);
542 if (ir->nstcalcenergy > 0)
544 if (ir->efep != efepNO)
546 /* nstdhdl should be a multiple of nstcalcenergy */
547 check_nst("nstcalcenergy", ir->nstcalcenergy,
548 "nstdhdl", &ir->fepvals->nstdhdl, wi);
549 /* nstexpanded should be a multiple of nstcalcenergy */
550 check_nst("nstcalcenergy", ir->nstcalcenergy,
551 "nstexpanded", &ir->expandedvals->nstexpanded, wi);
553 /* for storing exact averages nstenergy should be
554 * a multiple of nstcalcenergy
556 check_nst("nstcalcenergy", ir->nstcalcenergy,
557 "nstenergy", &ir->nstenergy, wi);
561 if (ir->nsteps == 0 && !ir->bContinuation)
563 warning_note(wi, "For a correct single-point energy evaluation with nsteps = 0, use continuation = yes to avoid constraining the input coordinates.");
567 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
568 ir->bContinuation && ir->ld_seed != -1)
570 warning_note(wi, "You are doing a continuation with SD or BD, make sure that ld_seed is different from the previous run (using ld_seed=-1 will ensure this)");
576 sprintf(err_buf, "TPI only works with pbc = %s", epbc_names[epbcXYZ]);
577 CHECK(ir->ePBC != epbcXYZ);
578 sprintf(err_buf, "TPI only works with ns = %s", ens_names[ensGRID]);
579 CHECK(ir->ns_type != ensGRID);
580 sprintf(err_buf, "with TPI nstlist should be larger than zero");
581 CHECK(ir->nstlist <= 0);
582 sprintf(err_buf, "TPI does not work with full electrostatics other than PME");
583 CHECK(EEL_FULL(ir->coulombtype) && !EEL_PME(ir->coulombtype));
584 sprintf(err_buf, "TPI does not work (yet) with the Verlet cut-off scheme");
585 CHECK(ir->cutoff_scheme == ecutsVERLET);
589 if ( (opts->nshake > 0) && (opts->bMorse) )
592 "Using morse bond-potentials while constraining bonds is useless");
593 warning(wi, warn_buf);
596 if ((EI_SD(ir->eI) || ir->eI == eiBD) &&
597 ir->bContinuation && ir->ld_seed != -1)
599 warning_note(wi, "You are doing a continuation with SD or BD, make sure that ld_seed is different from the previous run (using ld_seed=-1 will ensure this)");
601 /* verify simulated tempering options */
605 gmx_bool bAllTempZero = TRUE;
606 for (i = 0; i < fep->n_lambda; i++)
608 sprintf(err_buf, "Entry %d for %s must be between 0 and 1, instead is %g", i, efpt_names[efptTEMPERATURE], fep->all_lambda[efptTEMPERATURE][i]);
609 CHECK((fep->all_lambda[efptTEMPERATURE][i] < 0) || (fep->all_lambda[efptTEMPERATURE][i] > 1));
610 if (fep->all_lambda[efptTEMPERATURE][i] > 0)
612 bAllTempZero = FALSE;
615 sprintf(err_buf, "if simulated tempering is on, temperature-lambdas may not be all zero");
616 CHECK(bAllTempZero == TRUE);
618 sprintf(err_buf, "Simulated tempering is currently only compatible with md-vv");
619 CHECK(ir->eI != eiVV);
621 /* check compatability of the temperature coupling with simulated tempering */
623 if (ir->etc == etcNOSEHOOVER)
625 sprintf(warn_buf, "Nose-Hoover based temperature control such as [%s] my not be entirelyconsistent with simulated tempering", etcoupl_names[ir->etc]);
626 warning_note(wi, warn_buf);
629 /* check that the temperatures make sense */
631 sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= than the simulated tempering lower temperature (%g)", ir->simtempvals->simtemp_high, ir->simtempvals->simtemp_low);
632 CHECK(ir->simtempvals->simtemp_high <= ir->simtempvals->simtemp_low);
634 sprintf(err_buf, "Higher simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_high);
635 CHECK(ir->simtempvals->simtemp_high <= 0);
637 sprintf(err_buf, "Lower simulated tempering temperature (%g) must be >= zero", ir->simtempvals->simtemp_low);
638 CHECK(ir->simtempvals->simtemp_low <= 0);
641 /* verify free energy options */
643 if (ir->efep != efepNO)
646 sprintf(err_buf, "The soft-core power is %d and can only be 1 or 2",
648 CHECK(fep->sc_alpha != 0 && fep->sc_power != 1 && fep->sc_power != 2);
650 sprintf(err_buf, "The soft-core sc-r-power is %d and can only be 6 or 48",
651 (int)fep->sc_r_power);
652 CHECK(fep->sc_alpha != 0 && fep->sc_r_power != 6.0 && fep->sc_r_power != 48.0);
654 sprintf(err_buf, "Can't use postive delta-lambda (%g) if initial state/lambda does not start at zero", fep->delta_lambda);
655 CHECK(fep->delta_lambda > 0 && ((fep->init_fep_state > 0) || (fep->init_lambda > 0)));
657 sprintf(err_buf, "Can't use postive delta-lambda (%g) with expanded ensemble simulations", fep->delta_lambda);
658 CHECK(fep->delta_lambda > 0 && (ir->efep == efepEXPANDED));
660 sprintf(err_buf, "Can only use expanded ensemble with md-vv (for now)");
661 CHECK(!(EI_VV(ir->eI)) && (ir->efep == efepEXPANDED));
663 sprintf(err_buf, "Free-energy not implemented for Ewald");
664 CHECK(ir->coulombtype == eelEWALD);
666 /* check validty of lambda inputs */
667 if (fep->n_lambda == 0)
669 /* Clear output in case of no states:*/
670 sprintf(err_buf, "init-lambda-state set to %d: no lambda states are defined.", fep->init_fep_state);
671 CHECK((fep->init_fep_state >= 0) && (fep->n_lambda == 0));
675 sprintf(err_buf, "initial thermodynamic state %d does not exist, only goes to %d", fep->init_fep_state, fep->n_lambda-1);
676 CHECK((fep->init_fep_state >= fep->n_lambda));
679 sprintf(err_buf, "Lambda state must be set, either with init-lambda-state or with init-lambda");
680 CHECK((fep->init_fep_state < 0) && (fep->init_lambda < 0));
682 sprintf(err_buf, "init-lambda=%g while init-lambda-state=%d. Lambda state must be set either with init-lambda-state or with init-lambda, but not both",
683 fep->init_lambda, fep->init_fep_state);
684 CHECK((fep->init_fep_state >= 0) && (fep->init_lambda >= 0));
688 if ((fep->init_lambda >= 0) && (fep->delta_lambda == 0))
692 for (i = 0; i < efptNR; i++)
694 if (fep->separate_dvdl[i])
699 if (n_lambda_terms > 1)
701 sprintf(warn_buf, "If lambda vector states (fep-lambdas, coul-lambdas etc.) are set, don't use init-lambda to set lambda state (except for slow growth). Use init-lambda-state instead.");
702 warning(wi, warn_buf);
705 if (n_lambda_terms < 2 && fep->n_lambda > 0)
708 "init-lambda is deprecated for setting lambda state (except for slow growth). Use init-lambda-state instead.");
712 for (j = 0; j < efptNR; j++)
714 for (i = 0; i < fep->n_lambda; i++)
716 sprintf(err_buf, "Entry %d for %s must be between 0 and 1, instead is %g", i, efpt_names[j], fep->all_lambda[j][i]);
717 CHECK((fep->all_lambda[j][i] < 0) || (fep->all_lambda[j][i] > 1));
721 if ((fep->sc_alpha > 0) && (!fep->bScCoul))
723 for (i = 0; i < fep->n_lambda; i++)
725 sprintf(err_buf, "For state %d, vdw-lambdas (%f) is changing with vdw softcore, while coul-lambdas (%f) is nonzero without coulomb softcore: this will lead to crashes, and is not supported.", i, fep->all_lambda[efptVDW][i],
726 fep->all_lambda[efptCOUL][i]);
727 CHECK((fep->sc_alpha > 0) &&
728 (((fep->all_lambda[efptCOUL][i] > 0.0) &&
729 (fep->all_lambda[efptCOUL][i] < 1.0)) &&
730 ((fep->all_lambda[efptVDW][i] > 0.0) &&
731 (fep->all_lambda[efptVDW][i] < 1.0))));
735 if ((fep->bScCoul) && (EEL_PME(ir->coulombtype)))
737 real sigma, lambda, r_sc;
740 /* Maximum estimate for A and B charges equal with lambda power 1 */
742 r_sc = pow(lambda*fep->sc_alpha*pow(sigma/ir->rcoulomb, fep->sc_r_power) + 1.0, 1.0/fep->sc_r_power);
743 sprintf(warn_buf, "With PME there is a minor soft core effect present at the cut-off, proportional to (LJsigma/rcoulomb)^%g. This could have a minor effect on energy conservation, but usually other effects dominate. With a common sigma value of %g nm the fraction of the particle-particle potential at the cut-off at lambda=%g is around %.1e, while ewald-rtol is %.1e.",
745 sigma, lambda, r_sc - 1.0, ir->ewald_rtol);
746 warning_note(wi, warn_buf);
749 /* Free Energy Checks -- In an ideal world, slow growth and FEP would
750 be treated differently, but that's the next step */
752 for (i = 0; i < efptNR; i++)
754 for (j = 0; j < fep->n_lambda; j++)
756 sprintf(err_buf, "%s[%d] must be between 0 and 1", efpt_names[i], j);
757 CHECK((fep->all_lambda[i][j] < 0) || (fep->all_lambda[i][j] > 1));
762 if ((ir->bSimTemp) || (ir->efep == efepEXPANDED))
765 expand = ir->expandedvals;
767 /* checking equilibration of weights inputs for validity */
769 sprintf(err_buf, "weight-equil-number-all-lambda (%d) is ignored if lmc-weights-equil is not equal to %s",
770 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
771 CHECK((expand->equil_n_at_lam > 0) && (expand->elmceq != elmceqNUMATLAM));
773 sprintf(err_buf, "weight-equil-number-samples (%d) is ignored if lmc-weights-equil is not equal to %s",
774 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
775 CHECK((expand->equil_samples > 0) && (expand->elmceq != elmceqSAMPLES));
777 sprintf(err_buf, "weight-equil-number-steps (%d) is ignored if lmc-weights-equil is not equal to %s",
778 expand->equil_steps, elmceq_names[elmceqSTEPS]);
779 CHECK((expand->equil_steps > 0) && (expand->elmceq != elmceqSTEPS));
781 sprintf(err_buf, "weight-equil-wl-delta (%d) is ignored if lmc-weights-equil is not equal to %s",
782 expand->equil_samples, elmceq_names[elmceqWLDELTA]);
783 CHECK((expand->equil_wl_delta > 0) && (expand->elmceq != elmceqWLDELTA));
785 sprintf(err_buf, "weight-equil-count-ratio (%f) is ignored if lmc-weights-equil is not equal to %s",
786 expand->equil_ratio, elmceq_names[elmceqRATIO]);
787 CHECK((expand->equil_ratio > 0) && (expand->elmceq != elmceqRATIO));
789 sprintf(err_buf, "weight-equil-number-all-lambda (%d) must be a positive integer if lmc-weights-equil=%s",
790 expand->equil_n_at_lam, elmceq_names[elmceqNUMATLAM]);
791 CHECK((expand->equil_n_at_lam <= 0) && (expand->elmceq == elmceqNUMATLAM));
793 sprintf(err_buf, "weight-equil-number-samples (%d) must be a positive integer if lmc-weights-equil=%s",
794 expand->equil_samples, elmceq_names[elmceqSAMPLES]);
795 CHECK((expand->equil_samples <= 0) && (expand->elmceq == elmceqSAMPLES));
797 sprintf(err_buf, "weight-equil-number-steps (%d) must be a positive integer if lmc-weights-equil=%s",
798 expand->equil_steps, elmceq_names[elmceqSTEPS]);
799 CHECK((expand->equil_steps <= 0) && (expand->elmceq == elmceqSTEPS));
801 sprintf(err_buf, "weight-equil-wl-delta (%f) must be > 0 if lmc-weights-equil=%s",
802 expand->equil_wl_delta, elmceq_names[elmceqWLDELTA]);
803 CHECK((expand->equil_wl_delta <= 0) && (expand->elmceq == elmceqWLDELTA));
805 sprintf(err_buf, "weight-equil-count-ratio (%f) must be > 0 if lmc-weights-equil=%s",
806 expand->equil_ratio, elmceq_names[elmceqRATIO]);
807 CHECK((expand->equil_ratio <= 0) && (expand->elmceq == elmceqRATIO));
809 sprintf(err_buf, "lmc-weights-equil=%s only possible when lmc-stats = %s or lmc-stats %s",
810 elmceq_names[elmceqWLDELTA], elamstats_names[elamstatsWL], elamstats_names[elamstatsWWL]);
811 CHECK((expand->elmceq == elmceqWLDELTA) && (!EWL(expand->elamstats)));
813 sprintf(err_buf, "lmc-repeats (%d) must be greater than 0", expand->lmc_repeats);
814 CHECK((expand->lmc_repeats <= 0));
815 sprintf(err_buf, "minimum-var-min (%d) must be greater than 0", expand->minvarmin);
816 CHECK((expand->minvarmin <= 0));
817 sprintf(err_buf, "weight-c-range (%d) must be greater or equal to 0", expand->c_range);
818 CHECK((expand->c_range < 0));
819 sprintf(err_buf, "init-lambda-state (%d) must be zero if lmc-forced-nstart (%d)> 0 and lmc-move != 'no'",
820 fep->init_fep_state, expand->lmc_forced_nstart);
821 CHECK((fep->init_fep_state != 0) && (expand->lmc_forced_nstart > 0) && (expand->elmcmove != elmcmoveNO));
822 sprintf(err_buf, "lmc-forced-nstart (%d) must not be negative", expand->lmc_forced_nstart);
823 CHECK((expand->lmc_forced_nstart < 0));
824 sprintf(err_buf, "init-lambda-state (%d) must be in the interval [0,number of lambdas)", fep->init_fep_state);
825 CHECK((fep->init_fep_state < 0) || (fep->init_fep_state >= fep->n_lambda));
827 sprintf(err_buf, "init-wl-delta (%f) must be greater than or equal to 0", expand->init_wl_delta);
828 CHECK((expand->init_wl_delta < 0));
829 sprintf(err_buf, "wl-ratio (%f) must be between 0 and 1", expand->wl_ratio);
830 CHECK((expand->wl_ratio <= 0) || (expand->wl_ratio >= 1));
831 sprintf(err_buf, "wl-scale (%f) must be between 0 and 1", expand->wl_scale);
832 CHECK((expand->wl_scale <= 0) || (expand->wl_scale >= 1));
834 /* if there is no temperature control, we need to specify an MC temperature */
835 sprintf(err_buf, "If there is no temperature control, and lmc-mcmove!= 'no',mc_temperature must be set to a positive number");
836 if (expand->nstTij > 0)
838 sprintf(err_buf, "nst-transition-matrix (%d) must be an integer multiple of nstlog (%d)",
839 expand->nstTij, ir->nstlog);
840 CHECK((mod(expand->nstTij, ir->nstlog) != 0));
845 sprintf(err_buf, "walls only work with pbc=%s", epbc_names[epbcXY]);
846 CHECK(ir->nwall && ir->ePBC != epbcXY);
849 if (ir->ePBC != epbcXYZ && ir->nwall != 2)
851 if (ir->ePBC == epbcNONE)
853 if (ir->epc != epcNO)
855 warning(wi, "Turning off pressure coupling for vacuum system");
861 sprintf(err_buf, "Can not have pressure coupling with pbc=%s",
862 epbc_names[ir->ePBC]);
863 CHECK(ir->epc != epcNO);
865 sprintf(err_buf, "Can not have Ewald with pbc=%s", epbc_names[ir->ePBC]);
866 CHECK(EEL_FULL(ir->coulombtype));
868 sprintf(err_buf, "Can not have dispersion correction with pbc=%s",
869 epbc_names[ir->ePBC]);
870 CHECK(ir->eDispCorr != edispcNO);
873 if (ir->rlist == 0.0)
875 sprintf(err_buf, "can only have neighborlist cut-off zero (=infinite)\n"
876 "with coulombtype = %s or coulombtype = %s\n"
877 "without periodic boundary conditions (pbc = %s) and\n"
878 "rcoulomb and rvdw set to zero",
879 eel_names[eelCUT], eel_names[eelUSER], epbc_names[epbcNONE]);
880 CHECK(((ir->coulombtype != eelCUT) && (ir->coulombtype != eelUSER)) ||
881 (ir->ePBC != epbcNONE) ||
882 (ir->rcoulomb != 0.0) || (ir->rvdw != 0.0));
886 warning_note(wi, "Simulating without cut-offs can be (slightly) faster with nstlist=0, nstype=simple and only one MPI rank");
891 if (ir->nstcomm == 0)
893 ir->comm_mode = ecmNO;
895 if (ir->comm_mode != ecmNO)
899 warning(wi, "If you want to remove the rotation around the center of mass, you should set comm_mode = Angular instead of setting nstcomm < 0. nstcomm is modified to its absolute value");
900 ir->nstcomm = abs(ir->nstcomm);
903 if (ir->nstcalcenergy > 0 && ir->nstcomm < ir->nstcalcenergy)
905 warning_note(wi, "nstcomm < nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy");
906 ir->nstcomm = ir->nstcalcenergy;
909 if (ir->comm_mode == ecmANGULAR)
911 sprintf(err_buf, "Can not remove the rotation around the center of mass with periodic molecules");
912 CHECK(ir->bPeriodicMols);
913 if (ir->ePBC != epbcNONE)
915 warning(wi, "Removing the rotation around the center of mass in a periodic system, this can lead to artifacts. Only use this on a single (cluster of) molecules. This cluster should not cross periodic boundaries.");
920 if (EI_STATE_VELOCITY(ir->eI) && ir->ePBC == epbcNONE && ir->comm_mode != ecmANGULAR)
922 warning_note(wi, "Tumbling and or flying ice-cubes: We are not removing rotation around center of mass in a non-periodic system. You should probably set comm_mode = ANGULAR.");
925 sprintf(err_buf, "Twin-range neighbour searching (NS) with simple NS"
926 " algorithm not implemented");
927 CHECK(((ir->rcoulomb > ir->rlist) || (ir->rvdw > ir->rlist))
928 && (ir->ns_type == ensSIMPLE));
930 /* TEMPERATURE COUPLING */
931 if (ir->etc == etcYES)
933 ir->etc = etcBERENDSEN;
934 warning_note(wi, "Old option for temperature coupling given: "
935 "changing \"yes\" to \"Berendsen\"\n");
938 if ((ir->etc == etcNOSEHOOVER) || (ir->epc == epcMTTK))
940 if (ir->opts.nhchainlength < 1)
942 sprintf(warn_buf, "number of Nose-Hoover chains (currently %d) cannot be less than 1,reset to 1\n", ir->opts.nhchainlength);
943 ir->opts.nhchainlength = 1;
944 warning(wi, warn_buf);
947 if (ir->etc == etcNOSEHOOVER && !EI_VV(ir->eI) && ir->opts.nhchainlength > 1)
949 warning_note(wi, "leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1");
950 ir->opts.nhchainlength = 1;
955 ir->opts.nhchainlength = 0;
958 if (ir->eI == eiVVAK)
960 sprintf(err_buf, "%s implemented primarily for validation, and requires nsttcouple = 1 and nstpcouple = 1.",
962 CHECK((ir->nsttcouple != 1) || (ir->nstpcouple != 1));
965 if (ETC_ANDERSEN(ir->etc))
967 sprintf(err_buf, "%s temperature control not supported for integrator %s.", etcoupl_names[ir->etc], ei_names[ir->eI]);
968 CHECK(!(EI_VV(ir->eI)));
970 if (ir->nstcomm > 0 && (ir->etc == etcANDERSEN))
972 sprintf(warn_buf, "Center of mass removal not necessary for %s. All velocities of coupled groups are rerandomized periodically, so flying ice cube errors will not occur.", etcoupl_names[ir->etc]);
973 warning_note(wi, warn_buf);
976 sprintf(err_buf, "nstcomm must be 1, not %d for %s, as velocities of atoms in coupled groups are randomized every time step", ir->nstcomm, etcoupl_names[ir->etc]);
977 CHECK(ir->nstcomm > 1 && (ir->etc == etcANDERSEN));
980 if (ir->etc == etcBERENDSEN)
982 sprintf(warn_buf, "The %s thermostat does not generate the correct kinetic energy distribution. You might want to consider using the %s thermostat.",
983 ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
984 warning_note(wi, warn_buf);
987 if ((ir->etc == etcNOSEHOOVER || ETC_ANDERSEN(ir->etc))
988 && ir->epc == epcBERENDSEN)
990 sprintf(warn_buf, "Using Berendsen pressure coupling invalidates the "
991 "true ensemble for the thermostat");
992 warning(wi, warn_buf);
995 /* PRESSURE COUPLING */
996 if (ir->epc == epcISOTROPIC)
998 ir->epc = epcBERENDSEN;
999 warning_note(wi, "Old option for pressure coupling given: "
1000 "changing \"Isotropic\" to \"Berendsen\"\n");
1003 if (ir->epc != epcNO)
1005 dt_pcoupl = ir->nstpcouple*ir->delta_t;
1007 sprintf(err_buf, "tau-p must be > 0 instead of %g\n", ir->tau_p);
1008 CHECK(ir->tau_p <= 0);
1010 if (ir->tau_p/dt_pcoupl < pcouple_min_integration_steps(ir->epc) - 10*GMX_REAL_EPS)
1012 sprintf(warn_buf, "For proper integration of the %s barostat, tau-p (%g) should be at least %d times larger than nstpcouple*dt (%g)",
1013 EPCOUPLTYPE(ir->epc), ir->tau_p, pcouple_min_integration_steps(ir->epc), dt_pcoupl);
1014 warning(wi, warn_buf);
1017 sprintf(err_buf, "compressibility must be > 0 when using pressure"
1018 " coupling %s\n", EPCOUPLTYPE(ir->epc));
1019 CHECK(ir->compress[XX][XX] < 0 || ir->compress[YY][YY] < 0 ||
1020 ir->compress[ZZ][ZZ] < 0 ||
1021 (trace(ir->compress) == 0 && ir->compress[YY][XX] <= 0 &&
1022 ir->compress[ZZ][XX] <= 0 && ir->compress[ZZ][YY] <= 0));
1024 if (epcPARRINELLORAHMAN == ir->epc && opts->bGenVel)
1027 "You are generating velocities so I am assuming you "
1028 "are equilibrating a system. You are using "
1029 "%s pressure coupling, but this can be "
1030 "unstable for equilibration. If your system crashes, try "
1031 "equilibrating first with Berendsen pressure coupling. If "
1032 "you are not equilibrating the system, you can probably "
1033 "ignore this warning.",
1034 epcoupl_names[ir->epc]);
1035 warning(wi, warn_buf);
1041 if (ir->epc > epcNO)
1043 if ((ir->epc != epcBERENDSEN) && (ir->epc != epcMTTK))
1045 warning_error(wi, "for md-vv and md-vv-avek, can only use Berendsen and Martyna-Tuckerman-Tobias-Klein (MTTK) equations for pressure control; MTTK is equivalent to Parrinello-Rahman.");
1051 if (ir->epc == epcMTTK)
1053 warning_error(wi, "MTTK pressure coupling requires a Velocity-verlet integrator");
1057 /* ELECTROSTATICS */
1058 /* More checks are in triple check (grompp.c) */
1060 if (ir->coulombtype == eelSWITCH)
1062 sprintf(warn_buf, "coulombtype = %s is only for testing purposes and can lead to serious "
1063 "artifacts, advice: use coulombtype = %s",
1064 eel_names[ir->coulombtype],
1065 eel_names[eelRF_ZERO]);
1066 warning(wi, warn_buf);
1069 if (ir->epsilon_r != 1 && ir->implicit_solvent == eisGBSA)
1071 sprintf(warn_buf, "epsilon-r = %g with GB implicit solvent, will use this value for inner dielectric", ir->epsilon_r);
1072 warning_note(wi, warn_buf);
1075 if (EEL_RF(ir->coulombtype) && ir->epsilon_rf == 1 && ir->epsilon_r != 1)
1077 sprintf(warn_buf, "epsilon-r = %g and epsilon-rf = 1 with reaction field, proceeding assuming old format and exchanging epsilon-r and epsilon-rf", ir->epsilon_r);
1078 warning(wi, warn_buf);
1079 ir->epsilon_rf = ir->epsilon_r;
1080 ir->epsilon_r = 1.0;
1083 if (ir->epsilon_r == 0)
1086 "It is pointless to use long-range or Generalized Born electrostatics with infinite relative permittivity."
1087 "Since you are effectively turning of electrostatics, a plain cutoff will be much faster.");
1088 CHECK(EEL_FULL(ir->coulombtype) || ir->implicit_solvent == eisGBSA);
1091 if (getenv("GMX_DO_GALACTIC_DYNAMICS") == NULL)
1093 sprintf(err_buf, "epsilon-r must be >= 0 instead of %g\n", ir->epsilon_r);
1094 CHECK(ir->epsilon_r < 0);
1097 if (EEL_RF(ir->coulombtype))
1099 /* reaction field (at the cut-off) */
1101 if (ir->coulombtype == eelRF_ZERO)
1103 sprintf(warn_buf, "With coulombtype = %s, epsilon-rf must be 0, assuming you meant epsilon_rf=0",
1104 eel_names[ir->coulombtype]);
1105 CHECK(ir->epsilon_rf != 0);
1106 ir->epsilon_rf = 0.0;
1109 sprintf(err_buf, "epsilon-rf must be >= epsilon-r");
1110 CHECK((ir->epsilon_rf < ir->epsilon_r && ir->epsilon_rf != 0) ||
1111 (ir->epsilon_r == 0));
1112 if (ir->epsilon_rf == ir->epsilon_r)
1114 sprintf(warn_buf, "Using epsilon-rf = epsilon-r with %s does not make sense",
1115 eel_names[ir->coulombtype]);
1116 warning(wi, warn_buf);
1119 /* Allow rlist>rcoulomb for tabulated long range stuff. This just
1120 * means the interaction is zero outside rcoulomb, but it helps to
1121 * provide accurate energy conservation.
1123 if (ir_coulomb_might_be_zero_at_cutoff(ir))
1125 if (ir_coulomb_switched(ir))
1128 "With coulombtype = %s rcoulomb_switch must be < rcoulomb. Or, better: Use the potential modifier options!",
1129 eel_names[ir->coulombtype]);
1130 CHECK(ir->rcoulomb_switch >= ir->rcoulomb);
1133 else if (ir->coulombtype == eelCUT || EEL_RF(ir->coulombtype))
1135 if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1137 sprintf(err_buf, "With coulombtype = %s, rcoulomb should be >= rlist unless you use a potential modifier",
1138 eel_names[ir->coulombtype]);
1139 CHECK(ir->rlist > ir->rcoulomb);
1143 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT)
1146 "Explicit switch/shift coulomb interactions cannot be used in combination with a secondary coulomb-modifier.");
1147 CHECK( ir->coulomb_modifier != eintmodNONE);
1149 if (ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1152 "Explicit switch/shift vdw interactions cannot be used in combination with a secondary vdw-modifier.");
1153 CHECK( ir->vdw_modifier != eintmodNONE);
1156 if (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT ||
1157 ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT)
1160 "The switch/shift interaction settings are just for compatibility; you will get better "
1161 "performance from applying potential modifiers to your interactions!\n");
1162 warning_note(wi, warn_buf);
1165 if (ir->coulombtype == eelPMESWITCH || ir->coulomb_modifier == eintmodPOTSWITCH)
1167 if (ir->rcoulomb_switch/ir->rcoulomb < 0.9499)
1169 real percentage = 100*(ir->rcoulomb-ir->rcoulomb_switch)/ir->rcoulomb;
1170 sprintf(warn_buf, "The switching range should be 5%% or less (currently %.2f%% using a switching range of %4f-%4f) for accurate electrostatic energies, energy conservation will be good regardless, since ewald_rtol = %g.",
1171 percentage, ir->rcoulomb_switch, ir->rcoulomb, ir->ewald_rtol);
1172 warning(wi, warn_buf);
1176 if (ir->vdwtype == evdwSWITCH || ir->vdw_modifier == eintmodPOTSWITCH)
1178 if (ir->rvdw_switch == 0)
1180 sprintf(warn_buf, "rvdw-switch is equal 0 even though you are using a switched Lennard-Jones potential. This suggests it was not set in the mdp, which can lead to large energy errors. In GROMACS, 0.05 to 0.1 nm is often a reasonable vdw switching range.");
1181 warning(wi, warn_buf);
1185 if (EEL_FULL(ir->coulombtype))
1187 if (ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSER ||
1188 ir->coulombtype == eelPMEUSERSWITCH)
1190 sprintf(err_buf, "With coulombtype = %s, rcoulomb must be <= rlist",
1191 eel_names[ir->coulombtype]);
1192 CHECK(ir->rcoulomb > ir->rlist);
1194 else if (ir->cutoff_scheme == ecutsGROUP && ir->coulomb_modifier == eintmodNONE)
1196 if (ir->coulombtype == eelPME || ir->coulombtype == eelP3M_AD)
1199 "With coulombtype = %s (without modifier), rcoulomb must be equal to rlist,\n"
1200 "or rlistlong if nstcalclr=1. For optimal energy conservation,consider using\n"
1201 "a potential modifier.", eel_names[ir->coulombtype]);
1202 if (ir->nstcalclr == 1)
1204 CHECK(ir->rcoulomb != ir->rlist && ir->rcoulomb != ir->rlistlong);
1208 CHECK(ir->rcoulomb != ir->rlist);
1214 if (EEL_PME(ir->coulombtype) || EVDW_PME(ir->vdwtype))
1216 if (ir->pme_order < 3)
1218 warning_error(wi, "pme-order can not be smaller than 3");
1222 if (ir->nwall == 2 && EEL_FULL(ir->coulombtype))
1224 if (ir->ewald_geometry == eewg3D)
1226 sprintf(warn_buf, "With pbc=%s you should use ewald-geometry=%s",
1227 epbc_names[ir->ePBC], eewg_names[eewg3DC]);
1228 warning(wi, warn_buf);
1230 /* This check avoids extra pbc coding for exclusion corrections */
1231 sprintf(err_buf, "wall-ewald-zfac should be >= 2");
1232 CHECK(ir->wall_ewald_zfac < 2);
1234 if ((ir->ewald_geometry == eewg3DC) && (ir->ePBC != epbcXY) &&
1235 EEL_FULL(ir->coulombtype))
1237 sprintf(warn_buf, "With %s and ewald_geometry = %s you should use pbc = %s",
1238 eel_names[ir->coulombtype], eewg_names[eewg3DC], epbc_names[epbcXY]);
1239 warning(wi, warn_buf);
1241 if ((ir->epsilon_surface != 0) && EEL_FULL(ir->coulombtype))
1243 if (ir->cutoff_scheme == ecutsVERLET)
1245 sprintf(warn_buf, "Since molecules/charge groups are broken using the Verlet scheme, you can not use a dipole correction to the %s electrostatics.",
1246 eel_names[ir->coulombtype]);
1247 warning(wi, warn_buf);
1251 sprintf(warn_buf, "Dipole corrections to %s electrostatics only work if all charge groups that can cross PBC boundaries are dipoles. If this is not the case set epsilon_surface to 0",
1252 eel_names[ir->coulombtype]);
1253 warning_note(wi, warn_buf);
1257 if (ir_vdw_switched(ir))
1259 sprintf(err_buf, "With switched vdw forces or potentials, rvdw-switch must be < rvdw");
1260 CHECK(ir->rvdw_switch >= ir->rvdw);
1262 if (ir->rvdw_switch < 0.5*ir->rvdw)
1264 sprintf(warn_buf, "You are applying a switch function to vdw forces or potentials from %g to %g nm, which is more than half the interaction range, whereas switch functions are intended to act only close to the cut-off.",
1265 ir->rvdw_switch, ir->rvdw);
1266 warning_note(wi, warn_buf);
1269 else if (ir->vdwtype == evdwCUT || ir->vdwtype == evdwPME)
1271 if (ir->cutoff_scheme == ecutsGROUP && ir->vdw_modifier == eintmodNONE)
1273 sprintf(err_buf, "With vdwtype = %s, rvdw must be >= rlist unless you use a potential modifier", evdw_names[ir->vdwtype]);
1274 CHECK(ir->rlist > ir->rvdw);
1278 if (ir->vdwtype == evdwPME)
1280 if (!(ir->vdw_modifier == eintmodNONE || ir->vdw_modifier == eintmodPOTSHIFT))
1282 sprintf(err_buf, "With vdwtype = %s, the only supported modifiers are %s a\
1284 evdw_names[ir->vdwtype],
1285 eintmod_names[eintmodPOTSHIFT],
1286 eintmod_names[eintmodNONE]);
1290 if (ir->cutoff_scheme == ecutsGROUP)
1292 if (((ir->coulomb_modifier != eintmodNONE && ir->rcoulomb == ir->rlist) ||
1293 (ir->vdw_modifier != eintmodNONE && ir->rvdw == ir->rlist)))
1295 warning_note(wi, "With exact cut-offs, rlist should be "
1296 "larger than rcoulomb and rvdw, so that there "
1297 "is a buffer region for particle motion "
1298 "between neighborsearch steps");
1301 if (ir_coulomb_is_zero_at_cutoff(ir) && ir->rlistlong <= ir->rcoulomb)
1303 sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rcoulomb.",
1304 IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
1305 warning_note(wi, warn_buf);
1307 if (ir_vdw_switched(ir) && (ir->rlistlong <= ir->rvdw))
1309 sprintf(warn_buf, "For energy conservation with switch/shift potentials, %s should be 0.1 to 0.3 nm larger than rvdw.",
1310 IR_TWINRANGE(*ir) ? "rlistlong" : "rlist");
1311 warning_note(wi, warn_buf);
1315 if (ir->vdwtype == evdwUSER && ir->eDispCorr != edispcNO)
1317 warning_note(wi, "You have selected user tables with dispersion correction, the dispersion will be corrected to -C6/r^6 beyond rvdw_switch (the tabulated interaction between rvdw_switch and rvdw will not be double counted). Make sure that you really want dispersion correction to -C6/r^6.");
1320 if (ir->eI == eiLBFGS && (ir->coulombtype == eelCUT || ir->vdwtype == evdwCUT)
1323 warning(wi, "For efficient BFGS minimization, use switch/shift/pme instead of cut-off.");
1326 if (ir->eI == eiLBFGS && ir->nbfgscorr <= 0)
1328 warning(wi, "Using L-BFGS with nbfgscorr<=0 just gets you steepest descent.");
1331 /* ENERGY CONSERVATION */
1332 if (ir_NVE(ir) && ir->cutoff_scheme == ecutsGROUP)
1334 if (!ir_vdw_might_be_zero_at_cutoff(ir) && ir->rvdw > 0 && ir->vdw_modifier == eintmodNONE)
1336 sprintf(warn_buf, "You are using a cut-off for VdW interactions with NVE, for good energy conservation use vdwtype = %s (possibly with DispCorr)",
1337 evdw_names[evdwSHIFT]);
1338 warning_note(wi, warn_buf);
1340 if (!ir_coulomb_might_be_zero_at_cutoff(ir) && ir->rcoulomb > 0)
1342 sprintf(warn_buf, "You are using a cut-off for electrostatics with NVE, for good energy conservation use coulombtype = %s or %s",
1343 eel_names[eelPMESWITCH], eel_names[eelRF_ZERO]);
1344 warning_note(wi, warn_buf);
1348 if (EI_VV(ir->eI) && IR_TWINRANGE(*ir) && ir->nstlist > 1)
1350 sprintf(warn_buf, "Twin-range multiple time stepping does not work with integrator %s.", ei_names[ir->eI]);
1351 warning_error(wi, warn_buf);
1354 /* IMPLICIT SOLVENT */
1355 if (ir->coulombtype == eelGB_NOTUSED)
1357 sprintf(warn_buf, "Invalid option %s for coulombtype",
1358 eel_names[ir->coulombtype]);
1359 warning_error(wi, warn_buf);
1362 if (ir->sa_algorithm == esaSTILL)
1364 sprintf(err_buf, "Still SA algorithm not available yet, use %s or %s instead\n", esa_names[esaAPPROX], esa_names[esaNO]);
1365 CHECK(ir->sa_algorithm == esaSTILL);
1368 if (ir->implicit_solvent == eisGBSA)
1370 sprintf(err_buf, "With GBSA implicit solvent, rgbradii must be equal to rlist.");
1371 CHECK(ir->rgbradii != ir->rlist);
1373 if (ir->coulombtype != eelCUT)
1375 sprintf(err_buf, "With GBSA, coulombtype must be equal to %s\n", eel_names[eelCUT]);
1376 CHECK(ir->coulombtype != eelCUT);
1378 if (ir->vdwtype != evdwCUT)
1380 sprintf(err_buf, "With GBSA, vdw-type must be equal to %s\n", evdw_names[evdwCUT]);
1381 CHECK(ir->vdwtype != evdwCUT);
1383 if (ir->nstgbradii < 1)
1385 sprintf(warn_buf, "Using GBSA with nstgbradii<1, setting nstgbradii=1");
1386 warning_note(wi, warn_buf);
1389 if (ir->sa_algorithm == esaNO)
1391 sprintf(warn_buf, "No SA (non-polar) calculation requested together with GB. Are you sure this is what you want?\n");
1392 warning_note(wi, warn_buf);
1394 if (ir->sa_surface_tension < 0 && ir->sa_algorithm != esaNO)
1396 sprintf(warn_buf, "Value of sa_surface_tension is < 0. Changing it to 2.05016 or 2.25936 kJ/nm^2/mol for Still and HCT/OBC respectively\n");
1397 warning_note(wi, warn_buf);
1399 if (ir->gb_algorithm == egbSTILL)
1401 ir->sa_surface_tension = 0.0049 * CAL2JOULE * 100;
1405 ir->sa_surface_tension = 0.0054 * CAL2JOULE * 100;
1408 if (ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO)
1410 sprintf(err_buf, "Surface tension set to 0 while SA-calculation requested\n");
1411 CHECK(ir->sa_surface_tension == 0 && ir->sa_algorithm != esaNO);
1418 if (ir->cutoff_scheme != ecutsGROUP)
1420 warning_error(wi, "AdresS simulation supports only cutoff-scheme=group");
1424 warning_error(wi, "AdresS simulation supports only stochastic dynamics");
1426 if (ir->epc != epcNO)
1428 warning_error(wi, "AdresS simulation does not support pressure coupling");
1430 if (EEL_FULL(ir->coulombtype))
1432 warning_error(wi, "AdresS simulation does not support long-range electrostatics");
1437 /* count the number of text elemets separated by whitespace in a string.
1438 str = the input string
1439 maxptr = the maximum number of allowed elements
1440 ptr = the output array of pointers to the first character of each element
1441 returns: the number of elements. */
1442 int str_nelem(const char *str, int maxptr, char *ptr[])
1447 copy0 = gmx_strdup(str);
1450 while (*copy != '\0')
1454 gmx_fatal(FARGS, "Too many groups on line: '%s' (max is %d)",
1462 while ((*copy != '\0') && !isspace(*copy))
1481 /* interpret a number of doubles from a string and put them in an array,
1482 after allocating space for them.
1483 str = the input string
1484 n = the (pre-allocated) number of doubles read
1485 r = the output array of doubles. */
1486 static void parse_n_real(char *str, int *n, real **r)
1491 *n = str_nelem(str, MAXPTR, ptr);
1494 for (i = 0; i < *n; i++)
1496 (*r)[i] = strtod(ptr[i], NULL);
1500 static void do_fep_params(t_inputrec *ir, char fep_lambda[][STRLEN], char weights[STRLEN])
1503 int i, j, max_n_lambda, nweights, nfep[efptNR];
1504 t_lambda *fep = ir->fepvals;
1505 t_expanded *expand = ir->expandedvals;
1506 real **count_fep_lambdas;
1507 gmx_bool bOneLambda = TRUE;
1509 snew(count_fep_lambdas, efptNR);
1511 /* FEP input processing */
1512 /* first, identify the number of lambda values for each type.
1513 All that are nonzero must have the same number */
1515 for (i = 0; i < efptNR; i++)
1517 parse_n_real(fep_lambda[i], &(nfep[i]), &(count_fep_lambdas[i]));
1520 /* now, determine the number of components. All must be either zero, or equal. */
1523 for (i = 0; i < efptNR; i++)
1525 if (nfep[i] > max_n_lambda)
1527 max_n_lambda = nfep[i]; /* here's a nonzero one. All of them
1528 must have the same number if its not zero.*/
1533 for (i = 0; i < efptNR; i++)
1537 ir->fepvals->separate_dvdl[i] = FALSE;
1539 else if (nfep[i] == max_n_lambda)
1541 if (i != efptTEMPERATURE) /* we treat this differently -- not really a reason to compute the derivative with
1542 respect to the temperature currently */
1544 ir->fepvals->separate_dvdl[i] = TRUE;
1549 gmx_fatal(FARGS, "Number of lambdas (%d) for FEP type %s not equal to number of other types (%d)",
1550 nfep[i], efpt_names[i], max_n_lambda);
1553 /* we don't print out dhdl if the temperature is changing, since we can't correctly define dhdl in this case */
1554 ir->fepvals->separate_dvdl[efptTEMPERATURE] = FALSE;
1556 /* the number of lambdas is the number we've read in, which is either zero
1557 or the same for all */
1558 fep->n_lambda = max_n_lambda;
1560 /* allocate space for the array of lambda values */
1561 snew(fep->all_lambda, efptNR);
1562 /* if init_lambda is defined, we need to set lambda */
1563 if ((fep->init_lambda > 0) && (fep->n_lambda == 0))
1565 ir->fepvals->separate_dvdl[efptFEP] = TRUE;
1567 /* otherwise allocate the space for all of the lambdas, and transfer the data */
1568 for (i = 0; i < efptNR; i++)
1570 snew(fep->all_lambda[i], fep->n_lambda);
1571 if (nfep[i] > 0) /* if it's zero, then the count_fep_lambda arrays
1574 for (j = 0; j < fep->n_lambda; j++)
1576 fep->all_lambda[i][j] = (double)count_fep_lambdas[i][j];
1578 sfree(count_fep_lambdas[i]);
1581 sfree(count_fep_lambdas);
1583 /* "fep-vals" is either zero or the full number. If zero, we'll need to define fep-lambdas for internal
1584 bookkeeping -- for now, init_lambda */
1586 if ((nfep[efptFEP] == 0) && (fep->init_lambda >= 0))
1588 for (i = 0; i < fep->n_lambda; i++)
1590 fep->all_lambda[efptFEP][i] = fep->init_lambda;
1594 /* check to see if only a single component lambda is defined, and soft core is defined.
1595 In this case, turn on coulomb soft core */
1597 if (max_n_lambda == 0)
1603 for (i = 0; i < efptNR; i++)
1605 if ((nfep[i] != 0) && (i != efptFEP))
1611 if ((bOneLambda) && (fep->sc_alpha > 0))
1613 fep->bScCoul = TRUE;
1616 /* Fill in the others with the efptFEP if they are not explicitly
1617 specified (i.e. nfep[i] == 0). This means if fep is not defined,
1618 they are all zero. */
1620 for (i = 0; i < efptNR; i++)
1622 if ((nfep[i] == 0) && (i != efptFEP))
1624 for (j = 0; j < fep->n_lambda; j++)
1626 fep->all_lambda[i][j] = fep->all_lambda[efptFEP][j];
1632 /* make it easier if sc_r_power = 48 by increasing it to the 4th power, to be in the right scale. */
1633 if (fep->sc_r_power == 48)
1635 if (fep->sc_alpha > 0.1)
1637 gmx_fatal(FARGS, "sc_alpha (%f) for sc_r_power = 48 should usually be between 0.001 and 0.004", fep->sc_alpha);
1641 expand = ir->expandedvals;
1642 /* now read in the weights */
1643 parse_n_real(weights, &nweights, &(expand->init_lambda_weights));
1646 snew(expand->init_lambda_weights, fep->n_lambda); /* initialize to zero */
1648 else if (nweights != fep->n_lambda)
1650 gmx_fatal(FARGS, "Number of weights (%d) is not equal to number of lambda values (%d)",
1651 nweights, fep->n_lambda);
1653 if ((expand->nstexpanded < 0) && (ir->efep != efepNO))
1655 expand->nstexpanded = fep->nstdhdl;
1656 /* if you don't specify nstexpanded when doing expanded ensemble free energy calcs, it is set to nstdhdl */
1658 if ((expand->nstexpanded < 0) && ir->bSimTemp)
1660 expand->nstexpanded = 2*(int)(ir->opts.tau_t[0]/ir->delta_t);
1661 /* if you don't specify nstexpanded when doing expanded ensemble simulated tempering, it is set to
1662 2*tau_t just to be careful so it's not to frequent */
1667 static void do_simtemp_params(t_inputrec *ir)
1670 snew(ir->simtempvals->temperatures, ir->fepvals->n_lambda);
1671 GetSimTemps(ir->fepvals->n_lambda, ir->simtempvals, ir->fepvals->all_lambda[efptTEMPERATURE]);
1676 static void do_wall_params(t_inputrec *ir,
1677 char *wall_atomtype, char *wall_density,
1681 char *names[MAXPTR];
1684 opts->wall_atomtype[0] = NULL;
1685 opts->wall_atomtype[1] = NULL;
1687 ir->wall_atomtype[0] = -1;
1688 ir->wall_atomtype[1] = -1;
1689 ir->wall_density[0] = 0;
1690 ir->wall_density[1] = 0;
1694 nstr = str_nelem(wall_atomtype, MAXPTR, names);
1695 if (nstr != ir->nwall)
1697 gmx_fatal(FARGS, "Expected %d elements for wall_atomtype, found %d",
1700 for (i = 0; i < ir->nwall; i++)
1702 opts->wall_atomtype[i] = gmx_strdup(names[i]);
1705 if (ir->wall_type == ewt93 || ir->wall_type == ewt104)
1707 nstr = str_nelem(wall_density, MAXPTR, names);
1708 if (nstr != ir->nwall)
1710 gmx_fatal(FARGS, "Expected %d elements for wall-density, found %d", ir->nwall, nstr);
1712 for (i = 0; i < ir->nwall; i++)
1714 sscanf(names[i], "%lf", &dbl);
1717 gmx_fatal(FARGS, "wall-density[%d] = %f\n", i, dbl);
1719 ir->wall_density[i] = dbl;
1725 static void add_wall_energrps(gmx_groups_t *groups, int nwall, t_symtab *symtab)
1733 srenew(groups->grpname, groups->ngrpname+nwall);
1734 grps = &(groups->grps[egcENER]);
1735 srenew(grps->nm_ind, grps->nr+nwall);
1736 for (i = 0; i < nwall; i++)
1738 sprintf(str, "wall%d", i);
1739 groups->grpname[groups->ngrpname] = put_symtab(symtab, str);
1740 grps->nm_ind[grps->nr++] = groups->ngrpname++;
1745 void read_expandedparams(int *ninp_p, t_inpfile **inp_p,
1746 t_expanded *expand, warninp_t wi)
1748 int ninp, nerror = 0;
1754 /* read expanded ensemble parameters */
1755 CCTYPE ("expanded ensemble variables");
1756 ITYPE ("nstexpanded", expand->nstexpanded, -1);
1757 EETYPE("lmc-stats", expand->elamstats, elamstats_names);
1758 EETYPE("lmc-move", expand->elmcmove, elmcmove_names);
1759 EETYPE("lmc-weights-equil", expand->elmceq, elmceq_names);
1760 ITYPE ("weight-equil-number-all-lambda", expand->equil_n_at_lam, -1);
1761 ITYPE ("weight-equil-number-samples", expand->equil_samples, -1);
1762 ITYPE ("weight-equil-number-steps", expand->equil_steps, -1);
1763 RTYPE ("weight-equil-wl-delta", expand->equil_wl_delta, -1);
1764 RTYPE ("weight-equil-count-ratio", expand->equil_ratio, -1);
1765 CCTYPE("Seed for Monte Carlo in lambda space");
1766 ITYPE ("lmc-seed", expand->lmc_seed, -1);
1767 RTYPE ("mc-temperature", expand->mc_temp, -1);
1768 ITYPE ("lmc-repeats", expand->lmc_repeats, 1);
1769 ITYPE ("lmc-gibbsdelta", expand->gibbsdeltalam, -1);
1770 ITYPE ("lmc-forced-nstart", expand->lmc_forced_nstart, 0);
1771 EETYPE("symmetrized-transition-matrix", expand->bSymmetrizedTMatrix, yesno_names);
1772 ITYPE("nst-transition-matrix", expand->nstTij, -1);
1773 ITYPE ("mininum-var-min", expand->minvarmin, 100); /*default is reasonable */
1774 ITYPE ("weight-c-range", expand->c_range, 0); /* default is just C=0 */
1775 RTYPE ("wl-scale", expand->wl_scale, 0.8);
1776 RTYPE ("wl-ratio", expand->wl_ratio, 0.8);
1777 RTYPE ("init-wl-delta", expand->init_wl_delta, 1.0);
1778 EETYPE("wl-oneovert", expand->bWLoneovert, yesno_names);
1786 /*! \brief Return whether an end state with the given coupling-lambda
1787 * value describes fully-interacting VDW.
1789 * \param[in] couple_lambda_value Enumeration ecouplam value describing the end state
1790 * \return Whether VDW is on (i.e. the user chose vdw or vdw-q in the .mdp file)
1792 static gmx_bool couple_lambda_has_vdw_on(int couple_lambda_value)
1794 return (couple_lambda_value == ecouplamVDW ||
1795 couple_lambda_value == ecouplamVDWQ);
1798 void get_ir(const char *mdparin, const char *mdparout,
1799 t_inputrec *ir, t_gromppopts *opts,
1803 double dumdub[2][6];
1807 char warn_buf[STRLEN];
1808 t_lambda *fep = ir->fepvals;
1809 t_expanded *expand = ir->expandedvals;
1811 init_inputrec_strings();
1812 inp = read_inpfile(mdparin, &ninp, wi);
1814 snew(dumstr[0], STRLEN);
1815 snew(dumstr[1], STRLEN);
1817 if (-1 == search_einp(ninp, inp, "cutoff-scheme"))
1820 "%s did not specify a value for the .mdp option "
1821 "\"cutoff-scheme\". Probably it was first intended for use "
1822 "with GROMACS before 4.6. In 4.6, the Verlet scheme was "
1823 "introduced, but the group scheme was still the default. "
1824 "The default is now the Verlet scheme, so you will observe "
1825 "different behaviour.", mdparin);
1826 warning_note(wi, warn_buf);
1829 /* ignore the following deprecated commands */
1832 REM_TYPE("domain-decomposition");
1833 REM_TYPE("andersen-seed");
1835 REM_TYPE("dihre-fc");
1836 REM_TYPE("dihre-tau");
1837 REM_TYPE("nstdihreout");
1838 REM_TYPE("nstcheckpoint");
1839 REM_TYPE("optimize-fft");
1841 /* replace the following commands with the clearer new versions*/
1842 REPL_TYPE("unconstrained-start", "continuation");
1843 REPL_TYPE("foreign-lambda", "fep-lambdas");
1844 REPL_TYPE("verlet-buffer-drift", "verlet-buffer-tolerance");
1845 REPL_TYPE("nstxtcout", "nstxout-compressed");
1846 REPL_TYPE("xtc-grps", "compressed-x-grps");
1847 REPL_TYPE("xtc-precision", "compressed-x-precision");
1849 CCTYPE ("VARIOUS PREPROCESSING OPTIONS");
1850 CTYPE ("Preprocessor information: use cpp syntax.");
1851 CTYPE ("e.g.: -I/home/joe/doe -I/home/mary/roe");
1852 STYPE ("include", opts->include, NULL);
1853 CTYPE ("e.g.: -DPOSRES -DFLEXIBLE (note these variable names are case sensitive)");
1854 STYPE ("define", opts->define, NULL);
1856 CCTYPE ("RUN CONTROL PARAMETERS");
1857 EETYPE("integrator", ir->eI, ei_names);
1858 CTYPE ("Start time and timestep in ps");
1859 RTYPE ("tinit", ir->init_t, 0.0);
1860 RTYPE ("dt", ir->delta_t, 0.001);
1861 STEPTYPE ("nsteps", ir->nsteps, 0);
1862 CTYPE ("For exact run continuation or redoing part of a run");
1863 STEPTYPE ("init-step", ir->init_step, 0);
1864 CTYPE ("Part index is updated automatically on checkpointing (keeps files separate)");
1865 ITYPE ("simulation-part", ir->simulation_part, 1);
1866 CTYPE ("mode for center of mass motion removal");
1867 EETYPE("comm-mode", ir->comm_mode, ecm_names);
1868 CTYPE ("number of steps for center of mass motion removal");
1869 ITYPE ("nstcomm", ir->nstcomm, 100);
1870 CTYPE ("group(s) for center of mass motion removal");
1871 STYPE ("comm-grps", is->vcm, NULL);
1873 CCTYPE ("LANGEVIN DYNAMICS OPTIONS");
1874 CTYPE ("Friction coefficient (amu/ps) and random seed");
1875 RTYPE ("bd-fric", ir->bd_fric, 0.0);
1876 STEPTYPE ("ld-seed", ir->ld_seed, -1);
1879 CCTYPE ("ENERGY MINIMIZATION OPTIONS");
1880 CTYPE ("Force tolerance and initial step-size");
1881 RTYPE ("emtol", ir->em_tol, 10.0);
1882 RTYPE ("emstep", ir->em_stepsize, 0.01);
1883 CTYPE ("Max number of iterations in relax-shells");
1884 ITYPE ("niter", ir->niter, 20);
1885 CTYPE ("Step size (ps^2) for minimization of flexible constraints");
1886 RTYPE ("fcstep", ir->fc_stepsize, 0);
1887 CTYPE ("Frequency of steepest descents steps when doing CG");
1888 ITYPE ("nstcgsteep", ir->nstcgsteep, 1000);
1889 ITYPE ("nbfgscorr", ir->nbfgscorr, 10);
1891 CCTYPE ("TEST PARTICLE INSERTION OPTIONS");
1892 RTYPE ("rtpi", ir->rtpi, 0.05);
1894 /* Output options */
1895 CCTYPE ("OUTPUT CONTROL OPTIONS");
1896 CTYPE ("Output frequency for coords (x), velocities (v) and forces (f)");
1897 ITYPE ("nstxout", ir->nstxout, 0);
1898 ITYPE ("nstvout", ir->nstvout, 0);
1899 ITYPE ("nstfout", ir->nstfout, 0);
1900 CTYPE ("Output frequency for energies to log file and energy file");
1901 ITYPE ("nstlog", ir->nstlog, 1000);
1902 ITYPE ("nstcalcenergy", ir->nstcalcenergy, 100);
1903 ITYPE ("nstenergy", ir->nstenergy, 1000);
1904 CTYPE ("Output frequency and precision for .xtc file");
1905 ITYPE ("nstxout-compressed", ir->nstxout_compressed, 0);
1906 RTYPE ("compressed-x-precision", ir->x_compression_precision, 1000.0);
1907 CTYPE ("This selects the subset of atoms for the compressed");
1908 CTYPE ("trajectory file. You can select multiple groups. By");
1909 CTYPE ("default, all atoms will be written.");
1910 STYPE ("compressed-x-grps", is->x_compressed_groups, NULL);
1911 CTYPE ("Selection of energy groups");
1912 STYPE ("energygrps", is->energy, NULL);
1914 /* Neighbor searching */
1915 CCTYPE ("NEIGHBORSEARCHING PARAMETERS");
1916 CTYPE ("cut-off scheme (Verlet: particle based cut-offs, group: using charge groups)");
1917 EETYPE("cutoff-scheme", ir->cutoff_scheme, ecutscheme_names);
1918 CTYPE ("nblist update frequency");
1919 ITYPE ("nstlist", ir->nstlist, 10);
1920 CTYPE ("ns algorithm (simple or grid)");
1921 EETYPE("ns-type", ir->ns_type, ens_names);
1922 CTYPE ("Periodic boundary conditions: xyz, no, xy");
1923 EETYPE("pbc", ir->ePBC, epbc_names);
1924 EETYPE("periodic-molecules", ir->bPeriodicMols, yesno_names);
1925 CTYPE ("Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,");
1926 CTYPE ("a value of -1 means: use rlist");
1927 RTYPE("verlet-buffer-tolerance", ir->verletbuf_tol, 0.005);
1928 CTYPE ("nblist cut-off");
1929 RTYPE ("rlist", ir->rlist, 1.0);
1930 CTYPE ("long-range cut-off for switched potentials");
1931 RTYPE ("rlistlong", ir->rlistlong, -1);
1932 ITYPE ("nstcalclr", ir->nstcalclr, -1);
1934 /* Electrostatics */
1935 CCTYPE ("OPTIONS FOR ELECTROSTATICS AND VDW");
1936 CTYPE ("Method for doing electrostatics");
1937 EETYPE("coulombtype", ir->coulombtype, eel_names);
1938 EETYPE("coulomb-modifier", ir->coulomb_modifier, eintmod_names);
1939 CTYPE ("cut-off lengths");
1940 RTYPE ("rcoulomb-switch", ir->rcoulomb_switch, 0.0);
1941 RTYPE ("rcoulomb", ir->rcoulomb, 1.0);
1942 CTYPE ("Relative dielectric constant for the medium and the reaction field");
1943 RTYPE ("epsilon-r", ir->epsilon_r, 1.0);
1944 RTYPE ("epsilon-rf", ir->epsilon_rf, 0.0);
1945 CTYPE ("Method for doing Van der Waals");
1946 EETYPE("vdw-type", ir->vdwtype, evdw_names);
1947 EETYPE("vdw-modifier", ir->vdw_modifier, eintmod_names);
1948 CTYPE ("cut-off lengths");
1949 RTYPE ("rvdw-switch", ir->rvdw_switch, 0.0);
1950 RTYPE ("rvdw", ir->rvdw, 1.0);
1951 CTYPE ("Apply long range dispersion corrections for Energy and Pressure");
1952 EETYPE("DispCorr", ir->eDispCorr, edispc_names);
1953 CTYPE ("Extension of the potential lookup tables beyond the cut-off");
1954 RTYPE ("table-extension", ir->tabext, 1.0);
1955 CTYPE ("Separate tables between energy group pairs");
1956 STYPE ("energygrp-table", is->egptable, NULL);
1957 CTYPE ("Spacing for the PME/PPPM FFT grid");
1958 RTYPE ("fourierspacing", ir->fourier_spacing, 0.12);
1959 CTYPE ("FFT grid size, when a value is 0 fourierspacing will be used");
1960 ITYPE ("fourier-nx", ir->nkx, 0);
1961 ITYPE ("fourier-ny", ir->nky, 0);
1962 ITYPE ("fourier-nz", ir->nkz, 0);
1963 CTYPE ("EWALD/PME/PPPM parameters");
1964 ITYPE ("pme-order", ir->pme_order, 4);
1965 RTYPE ("ewald-rtol", ir->ewald_rtol, 0.00001);
1966 RTYPE ("ewald-rtol-lj", ir->ewald_rtol_lj, 0.001);
1967 EETYPE("lj-pme-comb-rule", ir->ljpme_combination_rule, eljpme_names);
1968 EETYPE("ewald-geometry", ir->ewald_geometry, eewg_names);
1969 RTYPE ("epsilon-surface", ir->epsilon_surface, 0.0);
1971 CCTYPE("IMPLICIT SOLVENT ALGORITHM");
1972 EETYPE("implicit-solvent", ir->implicit_solvent, eis_names);
1974 CCTYPE ("GENERALIZED BORN ELECTROSTATICS");
1975 CTYPE ("Algorithm for calculating Born radii");
1976 EETYPE("gb-algorithm", ir->gb_algorithm, egb_names);
1977 CTYPE ("Frequency of calculating the Born radii inside rlist");
1978 ITYPE ("nstgbradii", ir->nstgbradii, 1);
1979 CTYPE ("Cutoff for Born radii calculation; the contribution from atoms");
1980 CTYPE ("between rlist and rgbradii is updated every nstlist steps");
1981 RTYPE ("rgbradii", ir->rgbradii, 1.0);
1982 CTYPE ("Dielectric coefficient of the implicit solvent");
1983 RTYPE ("gb-epsilon-solvent", ir->gb_epsilon_solvent, 80.0);
1984 CTYPE ("Salt concentration in M for Generalized Born models");
1985 RTYPE ("gb-saltconc", ir->gb_saltconc, 0.0);
1986 CTYPE ("Scaling factors used in the OBC GB model. Default values are OBC(II)");
1987 RTYPE ("gb-obc-alpha", ir->gb_obc_alpha, 1.0);
1988 RTYPE ("gb-obc-beta", ir->gb_obc_beta, 0.8);
1989 RTYPE ("gb-obc-gamma", ir->gb_obc_gamma, 4.85);
1990 RTYPE ("gb-dielectric-offset", ir->gb_dielectric_offset, 0.009);
1991 EETYPE("sa-algorithm", ir->sa_algorithm, esa_names);
1992 CTYPE ("Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA");
1993 CTYPE ("The value -1 will set default value for Still/HCT/OBC GB-models.");
1994 RTYPE ("sa-surface-tension", ir->sa_surface_tension, -1);
1996 /* Coupling stuff */
1997 CCTYPE ("OPTIONS FOR WEAK COUPLING ALGORITHMS");
1998 CTYPE ("Temperature coupling");
1999 EETYPE("tcoupl", ir->etc, etcoupl_names);
2000 ITYPE ("nsttcouple", ir->nsttcouple, -1);
2001 ITYPE("nh-chain-length", ir->opts.nhchainlength, 10);
2002 EETYPE("print-nose-hoover-chain-variables", ir->bPrintNHChains, yesno_names);
2003 CTYPE ("Groups to couple separately");
2004 STYPE ("tc-grps", is->tcgrps, NULL);
2005 CTYPE ("Time constant (ps) and reference temperature (K)");
2006 STYPE ("tau-t", is->tau_t, NULL);
2007 STYPE ("ref-t", is->ref_t, NULL);
2008 CTYPE ("pressure coupling");
2009 EETYPE("pcoupl", ir->epc, epcoupl_names);
2010 EETYPE("pcoupltype", ir->epct, epcoupltype_names);
2011 ITYPE ("nstpcouple", ir->nstpcouple, -1);
2012 CTYPE ("Time constant (ps), compressibility (1/bar) and reference P (bar)");
2013 RTYPE ("tau-p", ir->tau_p, 1.0);
2014 STYPE ("compressibility", dumstr[0], NULL);
2015 STYPE ("ref-p", dumstr[1], NULL);
2016 CTYPE ("Scaling of reference coordinates, No, All or COM");
2017 EETYPE ("refcoord-scaling", ir->refcoord_scaling, erefscaling_names);
2020 CCTYPE ("OPTIONS FOR QMMM calculations");
2021 EETYPE("QMMM", ir->bQMMM, yesno_names);
2022 CTYPE ("Groups treated Quantum Mechanically");
2023 STYPE ("QMMM-grps", is->QMMM, NULL);
2024 CTYPE ("QM method");
2025 STYPE("QMmethod", is->QMmethod, NULL);
2026 CTYPE ("QMMM scheme");
2027 EETYPE("QMMMscheme", ir->QMMMscheme, eQMMMscheme_names);
2028 CTYPE ("QM basisset");
2029 STYPE("QMbasis", is->QMbasis, NULL);
2030 CTYPE ("QM charge");
2031 STYPE ("QMcharge", is->QMcharge, NULL);
2032 CTYPE ("QM multiplicity");
2033 STYPE ("QMmult", is->QMmult, NULL);
2034 CTYPE ("Surface Hopping");
2035 STYPE ("SH", is->bSH, NULL);
2036 CTYPE ("CAS space options");
2037 STYPE ("CASorbitals", is->CASorbitals, NULL);
2038 STYPE ("CASelectrons", is->CASelectrons, NULL);
2039 STYPE ("SAon", is->SAon, NULL);
2040 STYPE ("SAoff", is->SAoff, NULL);
2041 STYPE ("SAsteps", is->SAsteps, NULL);
2042 CTYPE ("Scale factor for MM charges");
2043 RTYPE ("MMChargeScaleFactor", ir->scalefactor, 1.0);
2044 CTYPE ("Optimization of QM subsystem");
2045 STYPE ("bOPT", is->bOPT, NULL);
2046 STYPE ("bTS", is->bTS, NULL);
2048 /* Simulated annealing */
2049 CCTYPE("SIMULATED ANNEALING");
2050 CTYPE ("Type of annealing for each temperature group (no/single/periodic)");
2051 STYPE ("annealing", is->anneal, NULL);
2052 CTYPE ("Number of time points to use for specifying annealing in each group");
2053 STYPE ("annealing-npoints", is->anneal_npoints, NULL);
2054 CTYPE ("List of times at the annealing points for each group");
2055 STYPE ("annealing-time", is->anneal_time, NULL);
2056 CTYPE ("Temp. at each annealing point, for each group.");
2057 STYPE ("annealing-temp", is->anneal_temp, NULL);
2060 CCTYPE ("GENERATE VELOCITIES FOR STARTUP RUN");
2061 EETYPE("gen-vel", opts->bGenVel, yesno_names);
2062 RTYPE ("gen-temp", opts->tempi, 300.0);
2063 ITYPE ("gen-seed", opts->seed, -1);
2066 CCTYPE ("OPTIONS FOR BONDS");
2067 EETYPE("constraints", opts->nshake, constraints);
2068 CTYPE ("Type of constraint algorithm");
2069 EETYPE("constraint-algorithm", ir->eConstrAlg, econstr_names);
2070 CTYPE ("Do not constrain the start configuration");
2071 EETYPE("continuation", ir->bContinuation, yesno_names);
2072 CTYPE ("Use successive overrelaxation to reduce the number of shake iterations");
2073 EETYPE("Shake-SOR", ir->bShakeSOR, yesno_names);
2074 CTYPE ("Relative tolerance of shake");
2075 RTYPE ("shake-tol", ir->shake_tol, 0.0001);
2076 CTYPE ("Highest order in the expansion of the constraint coupling matrix");
2077 ITYPE ("lincs-order", ir->nProjOrder, 4);
2078 CTYPE ("Number of iterations in the final step of LINCS. 1 is fine for");
2079 CTYPE ("normal simulations, but use 2 to conserve energy in NVE runs.");
2080 CTYPE ("For energy minimization with constraints it should be 4 to 8.");
2081 ITYPE ("lincs-iter", ir->nLincsIter, 1);
2082 CTYPE ("Lincs will write a warning to the stderr if in one step a bond");
2083 CTYPE ("rotates over more degrees than");
2084 RTYPE ("lincs-warnangle", ir->LincsWarnAngle, 30.0);
2085 CTYPE ("Convert harmonic bonds to morse potentials");
2086 EETYPE("morse", opts->bMorse, yesno_names);
2088 /* Energy group exclusions */
2089 CCTYPE ("ENERGY GROUP EXCLUSIONS");
2090 CTYPE ("Pairs of energy groups for which all non-bonded interactions are excluded");
2091 STYPE ("energygrp-excl", is->egpexcl, NULL);
2095 CTYPE ("Number of walls, type, atom types, densities and box-z scale factor for Ewald");
2096 ITYPE ("nwall", ir->nwall, 0);
2097 EETYPE("wall-type", ir->wall_type, ewt_names);
2098 RTYPE ("wall-r-linpot", ir->wall_r_linpot, -1);
2099 STYPE ("wall-atomtype", is->wall_atomtype, NULL);
2100 STYPE ("wall-density", is->wall_density, NULL);
2101 RTYPE ("wall-ewald-zfac", ir->wall_ewald_zfac, 3);
2104 CCTYPE("COM PULLING");
2105 EETYPE("pull", ir->bPull, yesno_names);
2109 is->pull_grp = read_pullparams(&ninp, &inp, ir->pull, wi);
2112 /* Enforced rotation */
2113 CCTYPE("ENFORCED ROTATION");
2114 CTYPE("Enforced rotation: No or Yes");
2115 EETYPE("rotation", ir->bRot, yesno_names);
2119 is->rot_grp = read_rotparams(&ninp, &inp, ir->rot, wi);
2122 /* Interactive MD */
2124 CCTYPE("Group to display and/or manipulate in interactive MD session");
2125 STYPE ("IMD-group", is->imd_grp, NULL);
2126 if (is->imd_grp[0] != '\0')
2133 CCTYPE("NMR refinement stuff");
2134 CTYPE ("Distance restraints type: No, Simple or Ensemble");
2135 EETYPE("disre", ir->eDisre, edisre_names);
2136 CTYPE ("Force weighting of pairs in one distance restraint: Conservative or Equal");
2137 EETYPE("disre-weighting", ir->eDisreWeighting, edisreweighting_names);
2138 CTYPE ("Use sqrt of the time averaged times the instantaneous violation");
2139 EETYPE("disre-mixed", ir->bDisreMixed, yesno_names);
2140 RTYPE ("disre-fc", ir->dr_fc, 1000.0);
2141 RTYPE ("disre-tau", ir->dr_tau, 0.0);
2142 CTYPE ("Output frequency for pair distances to energy file");
2143 ITYPE ("nstdisreout", ir->nstdisreout, 100);
2144 CTYPE ("Orientation restraints: No or Yes");
2145 EETYPE("orire", opts->bOrire, yesno_names);
2146 CTYPE ("Orientation restraints force constant and tau for time averaging");
2147 RTYPE ("orire-fc", ir->orires_fc, 0.0);
2148 RTYPE ("orire-tau", ir->orires_tau, 0.0);
2149 STYPE ("orire-fitgrp", is->orirefitgrp, NULL);
2150 CTYPE ("Output frequency for trace(SD) and S to energy file");
2151 ITYPE ("nstorireout", ir->nstorireout, 100);
2153 /* free energy variables */
2154 CCTYPE ("Free energy variables");
2155 EETYPE("free-energy", ir->efep, efep_names);
2156 STYPE ("couple-moltype", is->couple_moltype, NULL);
2157 EETYPE("couple-lambda0", opts->couple_lam0, couple_lam);
2158 EETYPE("couple-lambda1", opts->couple_lam1, couple_lam);
2159 EETYPE("couple-intramol", opts->bCoupleIntra, yesno_names);
2161 RTYPE ("init-lambda", fep->init_lambda, -1); /* start with -1 so
2163 it was not entered */
2164 ITYPE ("init-lambda-state", fep->init_fep_state, -1);
2165 RTYPE ("delta-lambda", fep->delta_lambda, 0.0);
2166 ITYPE ("nstdhdl", fep->nstdhdl, 50);
2167 STYPE ("fep-lambdas", is->fep_lambda[efptFEP], NULL);
2168 STYPE ("mass-lambdas", is->fep_lambda[efptMASS], NULL);
2169 STYPE ("coul-lambdas", is->fep_lambda[efptCOUL], NULL);
2170 STYPE ("vdw-lambdas", is->fep_lambda[efptVDW], NULL);
2171 STYPE ("bonded-lambdas", is->fep_lambda[efptBONDED], NULL);
2172 STYPE ("restraint-lambdas", is->fep_lambda[efptRESTRAINT], NULL);
2173 STYPE ("temperature-lambdas", is->fep_lambda[efptTEMPERATURE], NULL);
2174 ITYPE ("calc-lambda-neighbors", fep->lambda_neighbors, 1);
2175 STYPE ("init-lambda-weights", is->lambda_weights, NULL);
2176 EETYPE("dhdl-print-energy", fep->edHdLPrintEnergy, edHdLPrintEnergy_names);
2177 RTYPE ("sc-alpha", fep->sc_alpha, 0.0);
2178 ITYPE ("sc-power", fep->sc_power, 1);
2179 RTYPE ("sc-r-power", fep->sc_r_power, 6.0);
2180 RTYPE ("sc-sigma", fep->sc_sigma, 0.3);
2181 EETYPE("sc-coul", fep->bScCoul, yesno_names);
2182 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2183 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2184 EETYPE("separate-dhdl-file", fep->separate_dhdl_file,
2185 separate_dhdl_file_names);
2186 EETYPE("dhdl-derivatives", fep->dhdl_derivatives, dhdl_derivatives_names);
2187 ITYPE ("dh_hist_size", fep->dh_hist_size, 0);
2188 RTYPE ("dh_hist_spacing", fep->dh_hist_spacing, 0.1);
2190 /* Non-equilibrium MD stuff */
2191 CCTYPE("Non-equilibrium MD stuff");
2192 STYPE ("acc-grps", is->accgrps, NULL);
2193 STYPE ("accelerate", is->acc, NULL);
2194 STYPE ("freezegrps", is->freeze, NULL);
2195 STYPE ("freezedim", is->frdim, NULL);
2196 RTYPE ("cos-acceleration", ir->cos_accel, 0);
2197 STYPE ("deform", is->deform, NULL);
2199 /* simulated tempering variables */
2200 CCTYPE("simulated tempering variables");
2201 EETYPE("simulated-tempering", ir->bSimTemp, yesno_names);
2202 EETYPE("simulated-tempering-scaling", ir->simtempvals->eSimTempScale, esimtemp_names);
2203 RTYPE("sim-temp-low", ir->simtempvals->simtemp_low, 300.0);
2204 RTYPE("sim-temp-high", ir->simtempvals->simtemp_high, 300.0);
2206 /* expanded ensemble variables */
2207 if (ir->efep == efepEXPANDED || ir->bSimTemp)
2209 read_expandedparams(&ninp, &inp, expand, wi);
2212 /* Electric fields */
2213 CCTYPE("Electric fields");
2214 CTYPE ("Format is number of terms (int) and for all terms an amplitude (real)");
2215 CTYPE ("and a phase angle (real)");
2216 STYPE ("E-x", is->efield_x, NULL);
2217 CTYPE ("Time dependent (pulsed) electric field. Format is omega, time for pulse");
2218 CTYPE ("peak, and sigma (width) for pulse. Sigma = 0 removes pulse, leaving");
2219 CTYPE ("the field to be a cosine function.");
2220 STYPE ("E-xt", is->efield_xt, NULL);
2221 STYPE ("E-y", is->efield_y, NULL);
2222 STYPE ("E-yt", is->efield_yt, NULL);
2223 STYPE ("E-z", is->efield_z, NULL);
2224 STYPE ("E-zt", is->efield_zt, NULL);
2226 CCTYPE("Ion/water position swapping for computational electrophysiology setups");
2227 CTYPE("Swap positions along direction: no, X, Y, Z");
2228 EETYPE("swapcoords", ir->eSwapCoords, eSwapTypes_names);
2229 if (ir->eSwapCoords != eswapNO)
2232 CTYPE("Swap attempt frequency");
2233 ITYPE("swap-frequency", ir->swap->nstswap, 1);
2234 CTYPE("Two index groups that contain the compartment-partitioning atoms");
2235 STYPE("split-group0", splitgrp0, NULL);
2236 STYPE("split-group1", splitgrp1, NULL);
2237 CTYPE("Use center of mass of split groups (yes/no), otherwise center of geometry is used");
2238 EETYPE("massw-split0", ir->swap->massw_split[0], yesno_names);
2239 EETYPE("massw-split1", ir->swap->massw_split[1], yesno_names);
2241 CTYPE("Group name of ions that can be exchanged with solvent molecules");
2242 STYPE("swap-group", swapgrp, NULL);
2243 CTYPE("Group name of solvent molecules");
2244 STYPE("solvent-group", solgrp, NULL);
2246 CTYPE("Split cylinder: radius, upper and lower extension (nm) (this will define the channels)");
2247 CTYPE("Note that the split cylinder settings do not have an influence on the swapping protocol,");
2248 CTYPE("however, if correctly defined, the ion permeation events are counted per channel");
2249 RTYPE("cyl0-r", ir->swap->cyl0r, 2.0);
2250 RTYPE("cyl0-up", ir->swap->cyl0u, 1.0);
2251 RTYPE("cyl0-down", ir->swap->cyl0l, 1.0);
2252 RTYPE("cyl1-r", ir->swap->cyl1r, 2.0);
2253 RTYPE("cyl1-up", ir->swap->cyl1u, 1.0);
2254 RTYPE("cyl1-down", ir->swap->cyl1l, 1.0);
2256 CTYPE("Average the number of ions per compartment over these many swap attempt steps");
2257 ITYPE("coupl-steps", ir->swap->nAverage, 10);
2258 CTYPE("Requested number of anions and cations for each of the two compartments");
2259 CTYPE("-1 means fix the numbers as found in time step 0");
2260 ITYPE("anionsA", ir->swap->nanions[0], -1);
2261 ITYPE("cationsA", ir->swap->ncations[0], -1);
2262 ITYPE("anionsB", ir->swap->nanions[1], -1);
2263 ITYPE("cationsB", ir->swap->ncations[1], -1);
2264 CTYPE("Start to swap ions if threshold difference to requested count is reached");
2265 RTYPE("threshold", ir->swap->threshold, 1.0);
2268 /* AdResS defined thingies */
2269 CCTYPE ("AdResS parameters");
2270 EETYPE("adress", ir->bAdress, yesno_names);
2273 snew(ir->adress, 1);
2274 read_adressparams(&ninp, &inp, ir->adress, wi);
2277 /* User defined thingies */
2278 CCTYPE ("User defined thingies");
2279 STYPE ("user1-grps", is->user1, NULL);
2280 STYPE ("user2-grps", is->user2, NULL);
2281 ITYPE ("userint1", ir->userint1, 0);
2282 ITYPE ("userint2", ir->userint2, 0);
2283 ITYPE ("userint3", ir->userint3, 0);
2284 ITYPE ("userint4", ir->userint4, 0);
2285 RTYPE ("userreal1", ir->userreal1, 0);
2286 RTYPE ("userreal2", ir->userreal2, 0);
2287 RTYPE ("userreal3", ir->userreal3, 0);
2288 RTYPE ("userreal4", ir->userreal4, 0);
2291 write_inpfile(mdparout, ninp, inp, FALSE, wi);
2292 for (i = 0; (i < ninp); i++)
2295 sfree(inp[i].value);
2299 /* Process options if necessary */
2300 for (m = 0; m < 2; m++)
2302 for (i = 0; i < 2*DIM; i++)
2311 if (sscanf(dumstr[m], "%lf", &(dumdub[m][XX])) != 1)
2313 warning_error(wi, "Pressure coupling not enough values (I need 1)");
2315 dumdub[m][YY] = dumdub[m][ZZ] = dumdub[m][XX];
2317 case epctSEMIISOTROPIC:
2318 case epctSURFACETENSION:
2319 if (sscanf(dumstr[m], "%lf%lf",
2320 &(dumdub[m][XX]), &(dumdub[m][ZZ])) != 2)
2322 warning_error(wi, "Pressure coupling not enough values (I need 2)");
2324 dumdub[m][YY] = dumdub[m][XX];
2326 case epctANISOTROPIC:
2327 if (sscanf(dumstr[m], "%lf%lf%lf%lf%lf%lf",
2328 &(dumdub[m][XX]), &(dumdub[m][YY]), &(dumdub[m][ZZ]),
2329 &(dumdub[m][3]), &(dumdub[m][4]), &(dumdub[m][5])) != 6)
2331 warning_error(wi, "Pressure coupling not enough values (I need 6)");
2335 gmx_fatal(FARGS, "Pressure coupling type %s not implemented yet",
2336 epcoupltype_names[ir->epct]);
2340 clear_mat(ir->ref_p);
2341 clear_mat(ir->compress);
2342 for (i = 0; i < DIM; i++)
2344 ir->ref_p[i][i] = dumdub[1][i];
2345 ir->compress[i][i] = dumdub[0][i];
2347 if (ir->epct == epctANISOTROPIC)
2349 ir->ref_p[XX][YY] = dumdub[1][3];
2350 ir->ref_p[XX][ZZ] = dumdub[1][4];
2351 ir->ref_p[YY][ZZ] = dumdub[1][5];
2352 if (ir->ref_p[XX][YY] != 0 && ir->ref_p[XX][ZZ] != 0 && ir->ref_p[YY][ZZ] != 0)
2354 warning(wi, "All off-diagonal reference pressures are non-zero. Are you sure you want to apply a threefold shear stress?\n");
2356 ir->compress[XX][YY] = dumdub[0][3];
2357 ir->compress[XX][ZZ] = dumdub[0][4];
2358 ir->compress[YY][ZZ] = dumdub[0][5];
2359 for (i = 0; i < DIM; i++)
2361 for (m = 0; m < i; m++)
2363 ir->ref_p[i][m] = ir->ref_p[m][i];
2364 ir->compress[i][m] = ir->compress[m][i];
2369 if (ir->comm_mode == ecmNO)
2374 opts->couple_moltype = NULL;
2375 if (strlen(is->couple_moltype) > 0)
2377 if (ir->efep != efepNO)
2379 opts->couple_moltype = gmx_strdup(is->couple_moltype);
2380 if (opts->couple_lam0 == opts->couple_lam1)
2382 warning(wi, "The lambda=0 and lambda=1 states for coupling are identical");
2384 if (ir->eI == eiMD && (opts->couple_lam0 == ecouplamNONE ||
2385 opts->couple_lam1 == ecouplamNONE))
2387 warning(wi, "For proper sampling of the (nearly) decoupled state, stochastic dynamics should be used");
2392 warning_note(wi, "Free energy is turned off, so we will not decouple the molecule listed in your input.");
2395 /* FREE ENERGY AND EXPANDED ENSEMBLE OPTIONS */
2396 if (ir->efep != efepNO)
2398 if (fep->delta_lambda > 0)
2400 ir->efep = efepSLOWGROWTH;
2404 if (fep->edHdLPrintEnergy == edHdLPrintEnergyYES)
2406 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2407 warning_note(wi, "Old option for dhdl-print-energy given: "
2408 "changing \"yes\" to \"total\"\n");
2411 if (ir->bSimTemp && (fep->edHdLPrintEnergy == edHdLPrintEnergyNO))
2413 /* always print out the energy to dhdl if we are doing
2414 expanded ensemble, since we need the total energy for
2415 analysis if the temperature is changing. In some
2416 conditions one may only want the potential energy, so
2417 we will allow that if the appropriate mdp setting has
2418 been enabled. Otherwise, total it is:
2420 fep->edHdLPrintEnergy = edHdLPrintEnergyTOTAL;
2423 if ((ir->efep != efepNO) || ir->bSimTemp)
2425 ir->bExpanded = FALSE;
2426 if ((ir->efep == efepEXPANDED) || ir->bSimTemp)
2428 ir->bExpanded = TRUE;
2430 do_fep_params(ir, is->fep_lambda, is->lambda_weights);
2431 if (ir->bSimTemp) /* done after fep params */
2433 do_simtemp_params(ir);
2436 /* Because sc-coul (=FALSE by default) only acts on the lambda state
2437 * setup and not on the old way of specifying the free-energy setup,
2438 * we should check for using soft-core when not needed, since that
2439 * can complicate the sampling significantly.
2440 * Note that we only check for the automated coupling setup.
2441 * If the (advanced) user does FEP through manual topology changes,
2442 * this check will not be triggered.
2444 if (ir->efep != efepNO && ir->fepvals->n_lambda == 0 &&
2445 ir->fepvals->sc_alpha != 0 &&
2446 (couple_lambda_has_vdw_on(opts->couple_lam0) &&
2447 couple_lambda_has_vdw_on(opts->couple_lam1)))
2449 warning(wi, "You are using soft-core interactions while the Van der Waals interactions are not decoupled (note that the sc-coul option is only active when using lambda states). Although this will not lead to errors, you will need much more sampling than without soft-core interactions. Consider using sc-alpha=0.");
2454 ir->fepvals->n_lambda = 0;
2457 /* WALL PARAMETERS */
2459 do_wall_params(ir, is->wall_atomtype, is->wall_density, opts);
2461 /* ORIENTATION RESTRAINT PARAMETERS */
2463 if (opts->bOrire && str_nelem(is->orirefitgrp, MAXPTR, NULL) != 1)
2465 warning_error(wi, "ERROR: Need one orientation restraint fit group\n");
2468 /* DEFORMATION PARAMETERS */
2470 clear_mat(ir->deform);
2471 for (i = 0; i < 6; i++)
2475 m = sscanf(is->deform, "%lf %lf %lf %lf %lf %lf",
2476 &(dumdub[0][0]), &(dumdub[0][1]), &(dumdub[0][2]),
2477 &(dumdub[0][3]), &(dumdub[0][4]), &(dumdub[0][5]));
2478 for (i = 0; i < 3; i++)
2480 ir->deform[i][i] = dumdub[0][i];
2482 ir->deform[YY][XX] = dumdub[0][3];
2483 ir->deform[ZZ][XX] = dumdub[0][4];
2484 ir->deform[ZZ][YY] = dumdub[0][5];
2485 if (ir->epc != epcNO)
2487 for (i = 0; i < 3; i++)
2489 for (j = 0; j <= i; j++)
2491 if (ir->deform[i][j] != 0 && ir->compress[i][j] != 0)
2493 warning_error(wi, "A box element has deform set and compressibility > 0");
2497 for (i = 0; i < 3; i++)
2499 for (j = 0; j < i; j++)
2501 if (ir->deform[i][j] != 0)
2503 for (m = j; m < DIM; m++)
2505 if (ir->compress[m][j] != 0)
2507 sprintf(warn_buf, "An off-diagonal box element has deform set while compressibility > 0 for the same component of another box vector, this might lead to spurious periodicity effects.");
2508 warning(wi, warn_buf);
2516 /* Ion/water position swapping checks */
2517 if (ir->eSwapCoords != eswapNO)
2519 if (ir->swap->nstswap < 1)
2521 warning_error(wi, "swap_frequency must be 1 or larger when ion swapping is requested");
2523 if (ir->swap->nAverage < 1)
2525 warning_error(wi, "coupl_steps must be 1 or larger.\n");
2527 if (ir->swap->threshold < 1.0)
2529 warning_error(wi, "Ion count threshold must be at least 1.\n");
2537 static int search_QMstring(const char *s, int ng, const char *gn[])
2539 /* same as normal search_string, but this one searches QM strings */
2542 for (i = 0; (i < ng); i++)
2544 if (gmx_strcasecmp(s, gn[i]) == 0)
2550 gmx_fatal(FARGS, "this QM method or basisset (%s) is not implemented\n!", s);
2554 } /* search_QMstring */
2556 /* We would like gn to be const as well, but C doesn't allow this */
2557 /* TODO this is utility functionality (search for the index of a
2558 string in a collection), so should be refactored and located more
2560 int search_string(const char *s, int ng, char *gn[])
2564 for (i = 0; (i < ng); i++)
2566 if (gmx_strcasecmp(s, gn[i]) == 0)
2573 "Group %s referenced in the .mdp file was not found in the index file.\n"
2574 "Group names must match either [moleculetype] names or custom index group\n"
2575 "names, in which case you must supply an index file to the '-n' option\n"
2582 static gmx_bool do_numbering(int natoms, gmx_groups_t *groups, int ng, char *ptrs[],
2583 t_blocka *block, char *gnames[],
2584 int gtype, int restnm,
2585 int grptp, gmx_bool bVerbose,
2588 unsigned short *cbuf;
2589 t_grps *grps = &(groups->grps[gtype]);
2590 int i, j, gid, aj, ognr, ntot = 0;
2593 char warn_buf[STRLEN];
2597 fprintf(debug, "Starting numbering %d groups of type %d\n", ng, gtype);
2600 title = gtypes[gtype];
2603 /* Mark all id's as not set */
2604 for (i = 0; (i < natoms); i++)
2609 snew(grps->nm_ind, ng+1); /* +1 for possible rest group */
2610 for (i = 0; (i < ng); i++)
2612 /* Lookup the group name in the block structure */
2613 gid = search_string(ptrs[i], block->nr, gnames);
2614 if ((grptp != egrptpONE) || (i == 0))
2616 grps->nm_ind[grps->nr++] = gid;
2620 fprintf(debug, "Found gid %d for group %s\n", gid, ptrs[i]);
2623 /* Now go over the atoms in the group */
2624 for (j = block->index[gid]; (j < block->index[gid+1]); j++)
2629 /* Range checking */
2630 if ((aj < 0) || (aj >= natoms))
2632 gmx_fatal(FARGS, "Invalid atom number %d in indexfile", aj);
2634 /* Lookup up the old group number */
2638 gmx_fatal(FARGS, "Atom %d in multiple %s groups (%d and %d)",
2639 aj+1, title, ognr+1, i+1);
2643 /* Store the group number in buffer */
2644 if (grptp == egrptpONE)
2657 /* Now check whether we have done all atoms */
2661 if (grptp == egrptpALL)
2663 gmx_fatal(FARGS, "%d atoms are not part of any of the %s groups",
2664 natoms-ntot, title);
2666 else if (grptp == egrptpPART)
2668 sprintf(warn_buf, "%d atoms are not part of any of the %s groups",
2669 natoms-ntot, title);
2670 warning_note(wi, warn_buf);
2672 /* Assign all atoms currently unassigned to a rest group */
2673 for (j = 0; (j < natoms); j++)
2675 if (cbuf[j] == NOGID)
2681 if (grptp != egrptpPART)
2686 "Making dummy/rest group for %s containing %d elements\n",
2687 title, natoms-ntot);
2689 /* Add group name "rest" */
2690 grps->nm_ind[grps->nr] = restnm;
2692 /* Assign the rest name to all atoms not currently assigned to a group */
2693 for (j = 0; (j < natoms); j++)
2695 if (cbuf[j] == NOGID)
2704 if (grps->nr == 1 && (ntot == 0 || ntot == natoms))
2706 /* All atoms are part of one (or no) group, no index required */
2707 groups->ngrpnr[gtype] = 0;
2708 groups->grpnr[gtype] = NULL;
2712 groups->ngrpnr[gtype] = natoms;
2713 snew(groups->grpnr[gtype], natoms);
2714 for (j = 0; (j < natoms); j++)
2716 groups->grpnr[gtype][j] = cbuf[j];
2722 return (bRest && grptp == egrptpPART);
2725 static void calc_nrdf(gmx_mtop_t *mtop, t_inputrec *ir, char **gnames)
2728 gmx_groups_t *groups;
2729 pull_params_t *pull;
2730 int natoms, ai, aj, i, j, d, g, imin, jmin;
2732 int *nrdf2, *na_vcm, na_tot;
2733 double *nrdf_tc, *nrdf_vcm, nrdf_uc, n_sub = 0;
2734 gmx_mtop_atomloop_all_t aloop;
2736 int mb, mol, ftype, as;
2737 gmx_molblock_t *molb;
2738 gmx_moltype_t *molt;
2741 * First calc 3xnr-atoms for each group
2742 * then subtract half a degree of freedom for each constraint
2744 * Only atoms and nuclei contribute to the degrees of freedom...
2749 groups = &mtop->groups;
2750 natoms = mtop->natoms;
2752 /* Allocate one more for a possible rest group */
2753 /* We need to sum degrees of freedom into doubles,
2754 * since floats give too low nrdf's above 3 million atoms.
2756 snew(nrdf_tc, groups->grps[egcTC].nr+1);
2757 snew(nrdf_vcm, groups->grps[egcVCM].nr+1);
2758 snew(na_vcm, groups->grps[egcVCM].nr+1);
2760 for (i = 0; i < groups->grps[egcTC].nr; i++)
2764 for (i = 0; i < groups->grps[egcVCM].nr+1; i++)
2769 snew(nrdf2, natoms);
2770 aloop = gmx_mtop_atomloop_all_init(mtop);
2771 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
2774 if (atom->ptype == eptAtom || atom->ptype == eptNucleus)
2776 g = ggrpnr(groups, egcFREEZE, i);
2777 /* Double count nrdf for particle i */
2778 for (d = 0; d < DIM; d++)
2780 if (opts->nFreeze[g][d] == 0)
2785 nrdf_tc [ggrpnr(groups, egcTC, i)] += 0.5*nrdf2[i];
2786 nrdf_vcm[ggrpnr(groups, egcVCM, i)] += 0.5*nrdf2[i];
2791 for (mb = 0; mb < mtop->nmolblock; mb++)
2793 molb = &mtop->molblock[mb];
2794 molt = &mtop->moltype[molb->type];
2795 atom = molt->atoms.atom;
2796 for (mol = 0; mol < molb->nmol; mol++)
2798 for (ftype = F_CONSTR; ftype <= F_CONSTRNC; ftype++)
2800 ia = molt->ilist[ftype].iatoms;
2801 for (i = 0; i < molt->ilist[ftype].nr; )
2803 /* Subtract degrees of freedom for the constraints,
2804 * if the particles still have degrees of freedom left.
2805 * If one of the particles is a vsite or a shell, then all
2806 * constraint motion will go there, but since they do not
2807 * contribute to the constraints the degrees of freedom do not
2812 if (((atom[ia[1]].ptype == eptNucleus) ||
2813 (atom[ia[1]].ptype == eptAtom)) &&
2814 ((atom[ia[2]].ptype == eptNucleus) ||
2815 (atom[ia[2]].ptype == eptAtom)))
2833 imin = min(imin, nrdf2[ai]);
2834 jmin = min(jmin, nrdf2[aj]);
2837 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2838 nrdf_tc [ggrpnr(groups, egcTC, aj)] -= 0.5*jmin;
2839 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2840 nrdf_vcm[ggrpnr(groups, egcVCM, aj)] -= 0.5*jmin;
2842 ia += interaction_function[ftype].nratoms+1;
2843 i += interaction_function[ftype].nratoms+1;
2846 ia = molt->ilist[F_SETTLE].iatoms;
2847 for (i = 0; i < molt->ilist[F_SETTLE].nr; )
2849 /* Subtract 1 dof from every atom in the SETTLE */
2850 for (j = 0; j < 3; j++)
2853 imin = min(2, nrdf2[ai]);
2855 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2856 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2861 as += molt->atoms.nr;
2867 /* Correct nrdf for the COM constraints.
2868 * We correct using the TC and VCM group of the first atom
2869 * in the reference and pull group. If atoms in one pull group
2870 * belong to different TC or VCM groups it is anyhow difficult
2871 * to determine the optimal nrdf assignment.
2875 for (i = 0; i < pull->ncoord; i++)
2877 if (pull->coord[i].eType != epullCONSTRAINT)
2884 for (j = 0; j < 2; j++)
2886 const t_pull_group *pgrp;
2888 pgrp = &pull->group[pull->coord[i].group[j]];
2892 /* Subtract 1/2 dof from each group */
2894 nrdf_tc [ggrpnr(groups, egcTC, ai)] -= 0.5*imin;
2895 nrdf_vcm[ggrpnr(groups, egcVCM, ai)] -= 0.5*imin;
2896 if (nrdf_tc[ggrpnr(groups, egcTC, ai)] < 0)
2898 gmx_fatal(FARGS, "Center of mass pulling constraints caused the number of degrees of freedom for temperature coupling group %s to be negative", gnames[groups->grps[egcTC].nm_ind[ggrpnr(groups, egcTC, ai)]]);
2903 /* We need to subtract the whole DOF from group j=1 */
2910 if (ir->nstcomm != 0)
2912 /* Subtract 3 from the number of degrees of freedom in each vcm group
2913 * when com translation is removed and 6 when rotation is removed
2916 switch (ir->comm_mode)
2919 n_sub = ndof_com(ir);
2926 gmx_incons("Checking comm_mode");
2929 for (i = 0; i < groups->grps[egcTC].nr; i++)
2931 /* Count the number of atoms of TC group i for every VCM group */
2932 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2937 for (ai = 0; ai < natoms; ai++)
2939 if (ggrpnr(groups, egcTC, ai) == i)
2941 na_vcm[ggrpnr(groups, egcVCM, ai)]++;
2945 /* Correct for VCM removal according to the fraction of each VCM
2946 * group present in this TC group.
2948 nrdf_uc = nrdf_tc[i];
2951 fprintf(debug, "T-group[%d] nrdf_uc = %g, n_sub = %g\n",
2955 for (j = 0; j < groups->grps[egcVCM].nr+1; j++)
2957 if (nrdf_vcm[j] > n_sub)
2959 nrdf_tc[i] += nrdf_uc*((double)na_vcm[j]/(double)na_tot)*
2960 (nrdf_vcm[j] - n_sub)/nrdf_vcm[j];
2964 fprintf(debug, " nrdf_vcm[%d] = %g, nrdf = %g\n",
2965 j, nrdf_vcm[j], nrdf_tc[i]);
2970 for (i = 0; (i < groups->grps[egcTC].nr); i++)
2972 opts->nrdf[i] = nrdf_tc[i];
2973 if (opts->nrdf[i] < 0)
2978 "Number of degrees of freedom in T-Coupling group %s is %.2f\n",
2979 gnames[groups->grps[egcTC].nm_ind[i]], opts->nrdf[i]);
2988 static void decode_cos(char *s, t_cosines *cosine)
2991 char format[STRLEN], f1[STRLEN];
3003 sscanf(t, "%d", &(cosine->n));
3010 snew(cosine->a, cosine->n);
3011 snew(cosine->phi, cosine->n);
3013 sprintf(format, "%%*d");
3014 for (i = 0; (i < cosine->n); i++)
3017 strcat(f1, "%lf%lf");
3018 if (sscanf(t, f1, &a, &phi) < 2)
3020 gmx_fatal(FARGS, "Invalid input for electric field shift: '%s'", t);
3023 cosine->phi[i] = phi;
3024 strcat(format, "%*lf%*lf");
3031 static gmx_bool do_egp_flag(t_inputrec *ir, gmx_groups_t *groups,
3032 const char *option, const char *val, int flag)
3034 /* The maximum number of energy group pairs would be MAXPTR*(MAXPTR+1)/2.
3035 * But since this is much larger than STRLEN, such a line can not be parsed.
3036 * The real maximum is the number of names that fit in a string: STRLEN/2.
3038 #define EGP_MAX (STRLEN/2)
3039 int nelem, i, j, k, nr;
3040 char *names[EGP_MAX];
3044 gnames = groups->grpname;
3046 nelem = str_nelem(val, EGP_MAX, names);
3049 gmx_fatal(FARGS, "The number of groups for %s is odd", option);
3051 nr = groups->grps[egcENER].nr;
3053 for (i = 0; i < nelem/2; i++)
3057 gmx_strcasecmp(names[2*i], *(gnames[groups->grps[egcENER].nm_ind[j]])))
3063 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3064 names[2*i], option);
3068 gmx_strcasecmp(names[2*i+1], *(gnames[groups->grps[egcENER].nm_ind[k]])))
3074 gmx_fatal(FARGS, "%s in %s is not an energy group\n",
3075 names[2*i+1], option);
3077 if ((j < nr) && (k < nr))
3079 ir->opts.egp_flags[nr*j+k] |= flag;
3080 ir->opts.egp_flags[nr*k+j] |= flag;
3089 static void make_swap_groups(
3098 int ig = -1, i = 0, j;
3102 /* Just a quick check here, more thorough checks are in mdrun */
3103 if (strcmp(splitg0name, splitg1name) == 0)
3105 gmx_fatal(FARGS, "The split groups can not both be '%s'.", splitg0name);
3108 /* First get the swap group index atoms */
3109 ig = search_string(swapgname, grps->nr, gnames);
3110 swap->nat = grps->index[ig+1] - grps->index[ig];
3113 fprintf(stderr, "Swap group '%s' contains %d atoms.\n", swapgname, swap->nat);
3114 snew(swap->ind, swap->nat);
3115 for (i = 0; i < swap->nat; i++)
3117 swap->ind[i] = grps->a[grps->index[ig]+i];
3122 gmx_fatal(FARGS, "You defined an empty group of atoms for swapping.");
3125 /* Now do so for the split groups */
3126 for (j = 0; j < 2; j++)
3130 splitg = splitg0name;
3134 splitg = splitg1name;
3137 ig = search_string(splitg, grps->nr, gnames);
3138 swap->nat_split[j] = grps->index[ig+1] - grps->index[ig];
3139 if (swap->nat_split[j] > 0)
3141 fprintf(stderr, "Split group %d '%s' contains %d atom%s.\n",
3142 j, splitg, swap->nat_split[j], (swap->nat_split[j] > 1) ? "s" : "");
3143 snew(swap->ind_split[j], swap->nat_split[j]);
3144 for (i = 0; i < swap->nat_split[j]; i++)
3146 swap->ind_split[j][i] = grps->a[grps->index[ig]+i];
3151 gmx_fatal(FARGS, "Split group %d has to contain at least 1 atom!", j);
3155 /* Now get the solvent group index atoms */
3156 ig = search_string(solgname, grps->nr, gnames);
3157 swap->nat_sol = grps->index[ig+1] - grps->index[ig];
3158 if (swap->nat_sol > 0)
3160 fprintf(stderr, "Solvent group '%s' contains %d atoms.\n", solgname, swap->nat_sol);
3161 snew(swap->ind_sol, swap->nat_sol);
3162 for (i = 0; i < swap->nat_sol; i++)
3164 swap->ind_sol[i] = grps->a[grps->index[ig]+i];
3169 gmx_fatal(FARGS, "You defined an empty group of solvent. Cannot exchange ions.");
3174 void make_IMD_group(t_IMD *IMDgroup, char *IMDgname, t_blocka *grps, char **gnames)
3179 ig = search_string(IMDgname, grps->nr, gnames);
3180 IMDgroup->nat = grps->index[ig+1] - grps->index[ig];
3182 if (IMDgroup->nat > 0)
3184 fprintf(stderr, "Group '%s' with %d atoms can be activated for interactive molecular dynamics (IMD).\n",
3185 IMDgname, IMDgroup->nat);
3186 snew(IMDgroup->ind, IMDgroup->nat);
3187 for (i = 0; i < IMDgroup->nat; i++)
3189 IMDgroup->ind[i] = grps->a[grps->index[ig]+i];
3195 void do_index(const char* mdparin, const char *ndx,
3198 t_inputrec *ir, rvec *v,
3202 gmx_groups_t *groups;
3206 char warnbuf[STRLEN], **gnames;
3207 int nr, ntcg, ntau_t, nref_t, nacc, nofg, nSA, nSA_points, nSA_time, nSA_temp;
3210 int nacg, nfreeze, nfrdim, nenergy, nvcm, nuser;
3211 char *ptr1[MAXPTR], *ptr2[MAXPTR], *ptr3[MAXPTR];
3212 int i, j, k, restnm;
3214 gmx_bool bExcl, bTable, bSetTCpar, bAnneal, bRest;
3215 int nQMmethod, nQMbasis, nQMcharge, nQMmult, nbSH, nCASorb, nCASelec,
3216 nSAon, nSAoff, nSAsteps, nQMg, nbOPT, nbTS;
3217 char warn_buf[STRLEN];
3221 fprintf(stderr, "processing index file...\n");
3227 snew(grps->index, 1);
3229 atoms_all = gmx_mtop_global_atoms(mtop);
3230 analyse(&atoms_all, grps, &gnames, FALSE, TRUE);
3231 free_t_atoms(&atoms_all, FALSE);
3235 grps = init_index(ndx, &gnames);
3238 groups = &mtop->groups;
3239 natoms = mtop->natoms;
3240 symtab = &mtop->symtab;
3242 snew(groups->grpname, grps->nr+1);
3244 for (i = 0; (i < grps->nr); i++)
3246 groups->grpname[i] = put_symtab(symtab, gnames[i]);
3248 groups->grpname[i] = put_symtab(symtab, "rest");
3250 srenew(gnames, grps->nr+1);
3251 gnames[restnm] = *(groups->grpname[i]);
3252 groups->ngrpname = grps->nr+1;
3254 set_warning_line(wi, mdparin, -1);
3256 ntau_t = str_nelem(is->tau_t, MAXPTR, ptr1);
3257 nref_t = str_nelem(is->ref_t, MAXPTR, ptr2);
3258 ntcg = str_nelem(is->tcgrps, MAXPTR, ptr3);
3259 if ((ntau_t != ntcg) || (nref_t != ntcg))
3261 gmx_fatal(FARGS, "Invalid T coupling input: %d groups, %d ref-t values and "
3262 "%d tau-t values", ntcg, nref_t, ntau_t);
3265 bSetTCpar = (ir->etc || EI_SD(ir->eI) || ir->eI == eiBD || EI_TPI(ir->eI));
3266 do_numbering(natoms, groups, ntcg, ptr3, grps, gnames, egcTC,
3267 restnm, bSetTCpar ? egrptpALL : egrptpALL_GENREST, bVerbose, wi);
3268 nr = groups->grps[egcTC].nr;
3270 snew(ir->opts.nrdf, nr);
3271 snew(ir->opts.tau_t, nr);
3272 snew(ir->opts.ref_t, nr);
3273 if (ir->eI == eiBD && ir->bd_fric == 0)
3275 fprintf(stderr, "bd-fric=0, so tau-t will be used as the inverse friction constant(s)\n");
3282 gmx_fatal(FARGS, "Not enough ref-t and tau-t values!");
3286 for (i = 0; (i < nr); i++)
3288 ir->opts.tau_t[i] = strtod(ptr1[i], NULL);
3289 if ((ir->eI == eiBD || ir->eI == eiSD2) && ir->opts.tau_t[i] <= 0)
3291 sprintf(warn_buf, "With integrator %s tau-t should be larger than 0", ei_names[ir->eI]);
3292 warning_error(wi, warn_buf);
3295 if (ir->etc != etcVRESCALE && ir->opts.tau_t[i] == 0)
3297 warning_note(wi, "tau-t = -1 is the value to signal that a group should not have temperature coupling. Treating your use of tau-t = 0 as if you used -1.");
3300 if (ir->opts.tau_t[i] >= 0)
3302 tau_min = min(tau_min, ir->opts.tau_t[i]);
3305 if (ir->etc != etcNO && ir->nsttcouple == -1)
3307 ir->nsttcouple = ir_optimal_nsttcouple(ir);
3312 if ((ir->etc == etcNOSEHOOVER) && (ir->epc == epcBERENDSEN))
3314 gmx_fatal(FARGS, "Cannot do Nose-Hoover temperature with Berendsen pressure control with md-vv; use either vrescale temperature with berendsen pressure or Nose-Hoover temperature with MTTK pressure");
3316 if ((ir->epc == epcMTTK) && (ir->etc > etcNO))
3318 if (ir->nstpcouple != ir->nsttcouple)
3320 int mincouple = min(ir->nstpcouple, ir->nsttcouple);
3321 ir->nstpcouple = ir->nsttcouple = mincouple;
3322 sprintf(warn_buf, "for current Trotter decomposition methods with vv, nsttcouple and nstpcouple must be equal. Both have been reset to min(nsttcouple,nstpcouple) = %d", mincouple);
3323 warning_note(wi, warn_buf);
3327 /* velocity verlet with averaged kinetic energy KE = 0.5*(v(t+1/2) - v(t-1/2)) is implemented
3328 primarily for testing purposes, and does not work with temperature coupling other than 1 */
3330 if (ETC_ANDERSEN(ir->etc))
3332 if (ir->nsttcouple != 1)
3335 sprintf(warn_buf, "Andersen temperature control methods assume nsttcouple = 1; there is no need for larger nsttcouple > 1, since no global parameters are computed. nsttcouple has been reset to 1");
3336 warning_note(wi, warn_buf);
3339 nstcmin = tcouple_min_integration_steps(ir->etc);
3342 if (tau_min/(ir->delta_t*ir->nsttcouple) < nstcmin - 10*GMX_REAL_EPS)
3344 sprintf(warn_buf, "For proper integration of the %s thermostat, tau-t (%g) should be at least %d times larger than nsttcouple*dt (%g)",
3345 ETCOUPLTYPE(ir->etc),
3347 ir->nsttcouple*ir->delta_t);
3348 warning(wi, warn_buf);
3351 for (i = 0; (i < nr); i++)
3353 ir->opts.ref_t[i] = strtod(ptr2[i], NULL);
3354 if (ir->opts.ref_t[i] < 0)
3356 gmx_fatal(FARGS, "ref-t for group %d negative", i);
3359 /* set the lambda mc temperature to the md integrator temperature (which should be defined
3360 if we are in this conditional) if mc_temp is negative */
3361 if (ir->expandedvals->mc_temp < 0)
3363 ir->expandedvals->mc_temp = ir->opts.ref_t[0]; /*for now, set to the first reft */
3367 /* Simulated annealing for each group. There are nr groups */
3368 nSA = str_nelem(is->anneal, MAXPTR, ptr1);
3369 if (nSA == 1 && (ptr1[0][0] == 'n' || ptr1[0][0] == 'N'))
3373 if (nSA > 0 && nSA != nr)
3375 gmx_fatal(FARGS, "Not enough annealing values: %d (for %d groups)\n", nSA, nr);
3379 snew(ir->opts.annealing, nr);
3380 snew(ir->opts.anneal_npoints, nr);
3381 snew(ir->opts.anneal_time, nr);
3382 snew(ir->opts.anneal_temp, nr);
3383 for (i = 0; i < nr; i++)
3385 ir->opts.annealing[i] = eannNO;
3386 ir->opts.anneal_npoints[i] = 0;
3387 ir->opts.anneal_time[i] = NULL;
3388 ir->opts.anneal_temp[i] = NULL;
3393 for (i = 0; i < nr; i++)
3395 if (ptr1[i][0] == 'n' || ptr1[i][0] == 'N')
3397 ir->opts.annealing[i] = eannNO;
3399 else if (ptr1[i][0] == 's' || ptr1[i][0] == 'S')
3401 ir->opts.annealing[i] = eannSINGLE;
3404 else if (ptr1[i][0] == 'p' || ptr1[i][0] == 'P')
3406 ir->opts.annealing[i] = eannPERIODIC;
3412 /* Read the other fields too */
3413 nSA_points = str_nelem(is->anneal_npoints, MAXPTR, ptr1);
3414 if (nSA_points != nSA)
3416 gmx_fatal(FARGS, "Found %d annealing-npoints values for %d groups\n", nSA_points, nSA);
3418 for (k = 0, i = 0; i < nr; i++)
3420 ir->opts.anneal_npoints[i] = strtol(ptr1[i], NULL, 10);
3421 if (ir->opts.anneal_npoints[i] == 1)
3423 gmx_fatal(FARGS, "Please specify at least a start and an end point for annealing\n");
3425 snew(ir->opts.anneal_time[i], ir->opts.anneal_npoints[i]);
3426 snew(ir->opts.anneal_temp[i], ir->opts.anneal_npoints[i]);
3427 k += ir->opts.anneal_npoints[i];
3430 nSA_time = str_nelem(is->anneal_time, MAXPTR, ptr1);
3433 gmx_fatal(FARGS, "Found %d annealing-time values, wanter %d\n", nSA_time, k);
3435 nSA_temp = str_nelem(is->anneal_temp, MAXPTR, ptr2);
3438 gmx_fatal(FARGS, "Found %d annealing-temp values, wanted %d\n", nSA_temp, k);
3441 for (i = 0, k = 0; i < nr; i++)
3444 for (j = 0; j < ir->opts.anneal_npoints[i]; j++)
3446 ir->opts.anneal_time[i][j] = strtod(ptr1[k], NULL);
3447 ir->opts.anneal_temp[i][j] = strtod(ptr2[k], NULL);
3450 if (ir->opts.anneal_time[i][0] > (ir->init_t+GMX_REAL_EPS))
3452 gmx_fatal(FARGS, "First time point for annealing > init_t.\n");
3458 if (ir->opts.anneal_time[i][j] < ir->opts.anneal_time[i][j-1])
3460 gmx_fatal(FARGS, "Annealing timepoints out of order: t=%f comes after t=%f\n",
3461 ir->opts.anneal_time[i][j], ir->opts.anneal_time[i][j-1]);
3464 if (ir->opts.anneal_temp[i][j] < 0)
3466 gmx_fatal(FARGS, "Found negative temperature in annealing: %f\n", ir->opts.anneal_temp[i][j]);
3471 /* Print out some summary information, to make sure we got it right */
3472 for (i = 0, k = 0; i < nr; i++)
3474 if (ir->opts.annealing[i] != eannNO)
3476 j = groups->grps[egcTC].nm_ind[i];
3477 fprintf(stderr, "Simulated annealing for group %s: %s, %d timepoints\n",
3478 *(groups->grpname[j]), eann_names[ir->opts.annealing[i]],
3479 ir->opts.anneal_npoints[i]);
3480 fprintf(stderr, "Time (ps) Temperature (K)\n");
3481 /* All terms except the last one */
3482 for (j = 0; j < (ir->opts.anneal_npoints[i]-1); j++)
3484 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3487 /* Finally the last one */
3488 j = ir->opts.anneal_npoints[i]-1;
3489 if (ir->opts.annealing[i] == eannSINGLE)
3491 fprintf(stderr, "%9.1f- %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3495 fprintf(stderr, "%9.1f %5.1f\n", ir->opts.anneal_time[i][j], ir->opts.anneal_temp[i][j]);
3496 if (fabs(ir->opts.anneal_temp[i][j]-ir->opts.anneal_temp[i][0]) > GMX_REAL_EPS)
3498 warning_note(wi, "There is a temperature jump when your annealing loops back.\n");
3509 make_pull_groups(ir->pull, is->pull_grp, grps, gnames);
3511 make_pull_coords(ir->pull);
3516 make_rotation_groups(ir->rot, is->rot_grp, grps, gnames);
3519 if (ir->eSwapCoords != eswapNO)
3521 make_swap_groups(ir->swap, swapgrp, splitgrp0, splitgrp1, solgrp, grps, gnames);
3524 /* Make indices for IMD session */
3527 make_IMD_group(ir->imd, is->imd_grp, grps, gnames);
3530 nacc = str_nelem(is->acc, MAXPTR, ptr1);
3531 nacg = str_nelem(is->accgrps, MAXPTR, ptr2);
3532 if (nacg*DIM != nacc)
3534 gmx_fatal(FARGS, "Invalid Acceleration input: %d groups and %d acc. values",
3537 do_numbering(natoms, groups, nacg, ptr2, grps, gnames, egcACC,
3538 restnm, egrptpALL_GENREST, bVerbose, wi);
3539 nr = groups->grps[egcACC].nr;
3540 snew(ir->opts.acc, nr);
3541 ir->opts.ngacc = nr;
3543 for (i = k = 0; (i < nacg); i++)
3545 for (j = 0; (j < DIM); j++, k++)
3547 ir->opts.acc[i][j] = strtod(ptr1[k], NULL);
3550 for (; (i < nr); i++)
3552 for (j = 0; (j < DIM); j++)
3554 ir->opts.acc[i][j] = 0;
3558 nfrdim = str_nelem(is->frdim, MAXPTR, ptr1);
3559 nfreeze = str_nelem(is->freeze, MAXPTR, ptr2);
3560 if (nfrdim != DIM*nfreeze)
3562 gmx_fatal(FARGS, "Invalid Freezing input: %d groups and %d freeze values",
3565 do_numbering(natoms, groups, nfreeze, ptr2, grps, gnames, egcFREEZE,
3566 restnm, egrptpALL_GENREST, bVerbose, wi);
3567 nr = groups->grps[egcFREEZE].nr;
3568 ir->opts.ngfrz = nr;
3569 snew(ir->opts.nFreeze, nr);
3570 for (i = k = 0; (i < nfreeze); i++)
3572 for (j = 0; (j < DIM); j++, k++)
3574 ir->opts.nFreeze[i][j] = (gmx_strncasecmp(ptr1[k], "Y", 1) == 0);
3575 if (!ir->opts.nFreeze[i][j])
3577 if (gmx_strncasecmp(ptr1[k], "N", 1) != 0)
3579 sprintf(warnbuf, "Please use Y(ES) or N(O) for freezedim only "
3580 "(not %s)", ptr1[k]);
3581 warning(wi, warn_buf);
3586 for (; (i < nr); i++)
3588 for (j = 0; (j < DIM); j++)
3590 ir->opts.nFreeze[i][j] = 0;
3594 nenergy = str_nelem(is->energy, MAXPTR, ptr1);
3595 do_numbering(natoms, groups, nenergy, ptr1, grps, gnames, egcENER,
3596 restnm, egrptpALL_GENREST, bVerbose, wi);
3597 add_wall_energrps(groups, ir->nwall, symtab);
3598 ir->opts.ngener = groups->grps[egcENER].nr;
3599 nvcm = str_nelem(is->vcm, MAXPTR, ptr1);
3601 do_numbering(natoms, groups, nvcm, ptr1, grps, gnames, egcVCM,
3602 restnm, nvcm == 0 ? egrptpALL_GENREST : egrptpPART, bVerbose, wi);
3605 warning(wi, "Some atoms are not part of any center of mass motion removal group.\n"
3606 "This may lead to artifacts.\n"
3607 "In most cases one should use one group for the whole system.");
3610 /* Now we have filled the freeze struct, so we can calculate NRDF */
3611 calc_nrdf(mtop, ir, gnames);
3617 /* Must check per group! */
3618 for (i = 0; (i < ir->opts.ngtc); i++)
3620 ntot += ir->opts.nrdf[i];
3622 if (ntot != (DIM*natoms))
3624 fac = sqrt(ntot/(DIM*natoms));
3627 fprintf(stderr, "Scaling velocities by a factor of %.3f to account for constraints\n"
3628 "and removal of center of mass motion\n", fac);
3630 for (i = 0; (i < natoms); i++)
3632 svmul(fac, v[i], v[i]);
3637 nuser = str_nelem(is->user1, MAXPTR, ptr1);
3638 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser1,
3639 restnm, egrptpALL_GENREST, bVerbose, wi);
3640 nuser = str_nelem(is->user2, MAXPTR, ptr1);
3641 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcUser2,
3642 restnm, egrptpALL_GENREST, bVerbose, wi);
3643 nuser = str_nelem(is->x_compressed_groups, MAXPTR, ptr1);
3644 do_numbering(natoms, groups, nuser, ptr1, grps, gnames, egcCompressedX,
3645 restnm, egrptpONE, bVerbose, wi);
3646 nofg = str_nelem(is->orirefitgrp, MAXPTR, ptr1);
3647 do_numbering(natoms, groups, nofg, ptr1, grps, gnames, egcORFIT,
3648 restnm, egrptpALL_GENREST, bVerbose, wi);
3650 /* QMMM input processing */
3651 nQMg = str_nelem(is->QMMM, MAXPTR, ptr1);
3652 nQMmethod = str_nelem(is->QMmethod, MAXPTR, ptr2);
3653 nQMbasis = str_nelem(is->QMbasis, MAXPTR, ptr3);
3654 if ((nQMmethod != nQMg) || (nQMbasis != nQMg))
3656 gmx_fatal(FARGS, "Invalid QMMM input: %d groups %d basissets"
3657 " and %d methods\n", nQMg, nQMbasis, nQMmethod);
3659 /* group rest, if any, is always MM! */
3660 do_numbering(natoms, groups, nQMg, ptr1, grps, gnames, egcQMMM,
3661 restnm, egrptpALL_GENREST, bVerbose, wi);
3662 nr = nQMg; /*atoms->grps[egcQMMM].nr;*/
3663 ir->opts.ngQM = nQMg;
3664 snew(ir->opts.QMmethod, nr);
3665 snew(ir->opts.QMbasis, nr);
3666 for (i = 0; i < nr; i++)
3668 /* input consists of strings: RHF CASSCF PM3 .. These need to be
3669 * converted to the corresponding enum in names.c
3671 ir->opts.QMmethod[i] = search_QMstring(ptr2[i], eQMmethodNR,
3673 ir->opts.QMbasis[i] = search_QMstring(ptr3[i], eQMbasisNR,
3677 nQMmult = str_nelem(is->QMmult, MAXPTR, ptr1);
3678 nQMcharge = str_nelem(is->QMcharge, MAXPTR, ptr2);
3679 nbSH = str_nelem(is->bSH, MAXPTR, ptr3);
3680 snew(ir->opts.QMmult, nr);
3681 snew(ir->opts.QMcharge, nr);
3682 snew(ir->opts.bSH, nr);
3684 for (i = 0; i < nr; i++)
3686 ir->opts.QMmult[i] = strtol(ptr1[i], NULL, 10);
3687 ir->opts.QMcharge[i] = strtol(ptr2[i], NULL, 10);
3688 ir->opts.bSH[i] = (gmx_strncasecmp(ptr3[i], "Y", 1) == 0);
3691 nCASelec = str_nelem(is->CASelectrons, MAXPTR, ptr1);
3692 nCASorb = str_nelem(is->CASorbitals, MAXPTR, ptr2);
3693 snew(ir->opts.CASelectrons, nr);
3694 snew(ir->opts.CASorbitals, nr);
3695 for (i = 0; i < nr; i++)
3697 ir->opts.CASelectrons[i] = strtol(ptr1[i], NULL, 10);
3698 ir->opts.CASorbitals[i] = strtol(ptr2[i], NULL, 10);
3700 /* special optimization options */
3702 nbOPT = str_nelem(is->bOPT, MAXPTR, ptr1);
3703 nbTS = str_nelem(is->bTS, MAXPTR, ptr2);
3704 snew(ir->opts.bOPT, nr);
3705 snew(ir->opts.bTS, nr);
3706 for (i = 0; i < nr; i++)
3708 ir->opts.bOPT[i] = (gmx_strncasecmp(ptr1[i], "Y", 1) == 0);
3709 ir->opts.bTS[i] = (gmx_strncasecmp(ptr2[i], "Y", 1) == 0);
3711 nSAon = str_nelem(is->SAon, MAXPTR, ptr1);
3712 nSAoff = str_nelem(is->SAoff, MAXPTR, ptr2);
3713 nSAsteps = str_nelem(is->SAsteps, MAXPTR, ptr3);
3714 snew(ir->opts.SAon, nr);
3715 snew(ir->opts.SAoff, nr);
3716 snew(ir->opts.SAsteps, nr);
3718 for (i = 0; i < nr; i++)
3720 ir->opts.SAon[i] = strtod(ptr1[i], NULL);
3721 ir->opts.SAoff[i] = strtod(ptr2[i], NULL);
3722 ir->opts.SAsteps[i] = strtol(ptr3[i], NULL, 10);
3724 /* end of QMMM input */
3728 for (i = 0; (i < egcNR); i++)
3730 fprintf(stderr, "%-16s has %d element(s):", gtypes[i], groups->grps[i].nr);
3731 for (j = 0; (j < groups->grps[i].nr); j++)
3733 fprintf(stderr, " %s", *(groups->grpname[groups->grps[i].nm_ind[j]]));
3735 fprintf(stderr, "\n");
3739 nr = groups->grps[egcENER].nr;
3740 snew(ir->opts.egp_flags, nr*nr);
3742 bExcl = do_egp_flag(ir, groups, "energygrp-excl", is->egpexcl, EGP_EXCL);
3743 if (bExcl && ir->cutoff_scheme == ecutsVERLET)
3745 warning_error(wi, "Energy group exclusions are not (yet) implemented for the Verlet scheme");
3747 if (bExcl && EEL_FULL(ir->coulombtype))
3749 warning(wi, "Can not exclude the lattice Coulomb energy between energy groups");
3752 bTable = do_egp_flag(ir, groups, "energygrp-table", is->egptable, EGP_TABLE);
3753 if (bTable && !(ir->vdwtype == evdwUSER) &&
3754 !(ir->coulombtype == eelUSER) && !(ir->coulombtype == eelPMEUSER) &&
3755 !(ir->coulombtype == eelPMEUSERSWITCH))
3757 gmx_fatal(FARGS, "Can only have energy group pair tables in combination with user tables for VdW and/or Coulomb");
3760 decode_cos(is->efield_x, &(ir->ex[XX]));
3761 decode_cos(is->efield_xt, &(ir->et[XX]));
3762 decode_cos(is->efield_y, &(ir->ex[YY]));
3763 decode_cos(is->efield_yt, &(ir->et[YY]));
3764 decode_cos(is->efield_z, &(ir->ex[ZZ]));
3765 decode_cos(is->efield_zt, &(ir->et[ZZ]));
3769 do_adress_index(ir->adress, groups, gnames, &(ir->opts), wi);
3772 for (i = 0; (i < grps->nr); i++)
3784 static void check_disre(gmx_mtop_t *mtop)
3786 gmx_ffparams_t *ffparams;
3787 t_functype *functype;
3789 int i, ndouble, ftype;
3790 int label, old_label;
3792 if (gmx_mtop_ftype_count(mtop, F_DISRES) > 0)
3794 ffparams = &mtop->ffparams;
3795 functype = ffparams->functype;
3796 ip = ffparams->iparams;
3799 for (i = 0; i < ffparams->ntypes; i++)
3801 ftype = functype[i];
3802 if (ftype == F_DISRES)
3804 label = ip[i].disres.label;
3805 if (label == old_label)
3807 fprintf(stderr, "Distance restraint index %d occurs twice\n", label);
3815 gmx_fatal(FARGS, "Found %d double distance restraint indices,\n"
3816 "probably the parameters for multiple pairs in one restraint "
3817 "are not identical\n", ndouble);
3822 static gmx_bool absolute_reference(t_inputrec *ir, gmx_mtop_t *sys,
3823 gmx_bool posres_only,
3827 gmx_mtop_ilistloop_t iloop;
3837 for (d = 0; d < DIM; d++)
3839 AbsRef[d] = (d < ndof_com(ir) ? 0 : 1);
3841 /* Check for freeze groups */
3842 for (g = 0; g < ir->opts.ngfrz; g++)
3844 for (d = 0; d < DIM; d++)
3846 if (ir->opts.nFreeze[g][d] != 0)
3854 /* Check for position restraints */
3855 iloop = gmx_mtop_ilistloop_init(sys);
3856 while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
3859 (AbsRef[XX] == 0 || AbsRef[YY] == 0 || AbsRef[ZZ] == 0))
3861 for (i = 0; i < ilist[F_POSRES].nr; i += 2)
3863 pr = &sys->ffparams.iparams[ilist[F_POSRES].iatoms[i]];
3864 for (d = 0; d < DIM; d++)
3866 if (pr->posres.fcA[d] != 0)
3872 for (i = 0; i < ilist[F_FBPOSRES].nr; i += 2)
3874 /* Check for flat-bottom posres */
3875 pr = &sys->ffparams.iparams[ilist[F_FBPOSRES].iatoms[i]];
3876 if (pr->fbposres.k != 0)
3878 switch (pr->fbposres.geom)
3880 case efbposresSPHERE:
3881 AbsRef[XX] = AbsRef[YY] = AbsRef[ZZ] = 1;
3883 case efbposresCYLINDERX:
3884 AbsRef[YY] = AbsRef[ZZ] = 1;
3886 case efbposresCYLINDERY:
3887 AbsRef[XX] = AbsRef[ZZ] = 1;
3889 case efbposresCYLINDER:
3890 /* efbposres is a synonym for efbposresCYLINDERZ for backwards compatibility */
3891 case efbposresCYLINDERZ:
3892 AbsRef[XX] = AbsRef[YY] = 1;
3894 case efbposresX: /* d=XX */
3895 case efbposresY: /* d=YY */
3896 case efbposresZ: /* d=ZZ */
3897 d = pr->fbposres.geom - efbposresX;
3901 gmx_fatal(FARGS, " Invalid geometry for flat-bottom position restraint.\n"
3902 "Expected nr between 1 and %d. Found %d\n", efbposresNR-1,
3910 return (AbsRef[XX] != 0 && AbsRef[YY] != 0 && AbsRef[ZZ] != 0);
3914 check_combination_rule_differences(const gmx_mtop_t *mtop, int state,
3915 gmx_bool *bC6ParametersWorkWithGeometricRules,
3916 gmx_bool *bC6ParametersWorkWithLBRules,
3917 gmx_bool *bLBRulesPossible)
3919 int ntypes, tpi, tpj, thisLBdiff, thisgeomdiff;
3922 double geometricdiff, LBdiff;
3923 double c6i, c6j, c12i, c12j;
3924 double c6, c6_geometric, c6_LB;
3925 double sigmai, sigmaj, epsi, epsj;
3926 gmx_bool bCanDoLBRules, bCanDoGeometricRules;
3929 /* A tolerance of 1e-5 seems reasonable for (possibly hand-typed)
3930 * force-field floating point parameters.
3933 ptr = getenv("GMX_LJCOMB_TOL");
3938 sscanf(ptr, "%lf", &dbl);
3942 *bC6ParametersWorkWithLBRules = TRUE;
3943 *bC6ParametersWorkWithGeometricRules = TRUE;
3944 bCanDoLBRules = TRUE;
3945 bCanDoGeometricRules = TRUE;
3946 ntypes = mtop->ffparams.atnr;
3947 snew(typecount, ntypes);
3948 gmx_mtop_count_atomtypes(mtop, state, typecount);
3949 geometricdiff = LBdiff = 0.0;
3950 *bLBRulesPossible = TRUE;
3951 for (tpi = 0; tpi < ntypes; ++tpi)
3953 c6i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c6;
3954 c12i = mtop->ffparams.iparams[(ntypes + 1) * tpi].lj.c12;
3955 for (tpj = tpi; tpj < ntypes; ++tpj)
3957 c6j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c6;
3958 c12j = mtop->ffparams.iparams[(ntypes + 1) * tpj].lj.c12;
3959 c6 = mtop->ffparams.iparams[ntypes * tpi + tpj].lj.c6;
3960 c6_geometric = sqrt(c6i * c6j);
3961 if (!gmx_numzero(c6_geometric))
3963 if (!gmx_numzero(c12i) && !gmx_numzero(c12j))
3965 sigmai = pow(c12i / c6i, 1.0/6.0);
3966 sigmaj = pow(c12j / c6j, 1.0/6.0);
3967 epsi = c6i * c6i /(4.0 * c12i);
3968 epsj = c6j * c6j /(4.0 * c12j);
3969 c6_LB = 4.0 * pow(epsi * epsj, 1.0/2.0) * pow(0.5 * (sigmai + sigmaj), 6);
3973 *bLBRulesPossible = FALSE;
3974 c6_LB = c6_geometric;
3976 bCanDoLBRules = gmx_within_tol(c6_LB, c6, tol);
3979 if (FALSE == bCanDoLBRules)
3981 *bC6ParametersWorkWithLBRules = FALSE;
3984 bCanDoGeometricRules = gmx_within_tol(c6_geometric, c6, tol);
3986 if (FALSE == bCanDoGeometricRules)
3988 *bC6ParametersWorkWithGeometricRules = FALSE;
3996 check_combination_rules(const t_inputrec *ir, const gmx_mtop_t *mtop,
4000 gmx_bool bLBRulesPossible, bC6ParametersWorkWithGeometricRules, bC6ParametersWorkWithLBRules;
4002 check_combination_rule_differences(mtop, 0,
4003 &bC6ParametersWorkWithGeometricRules,
4004 &bC6ParametersWorkWithLBRules,
4006 if (ir->ljpme_combination_rule == eljpmeLB)
4008 if (FALSE == bC6ParametersWorkWithLBRules || FALSE == bLBRulesPossible)
4010 warning(wi, "You are using arithmetic-geometric combination rules "
4011 "in LJ-PME, but your non-bonded C6 parameters do not "
4012 "follow these rules.");
4017 if (FALSE == bC6ParametersWorkWithGeometricRules)
4019 if (ir->eDispCorr != edispcNO)
4021 warning_note(wi, "You are using geometric combination rules in "
4022 "LJ-PME, but your non-bonded C6 parameters do "
4023 "not follow these rules. "
4024 "This will introduce very small errors in the forces and energies in "
4025 "your simulations. Dispersion correction will correct total energy "
4026 "and/or pressure for isotropic systems, but not forces or surface tensions.");
4030 warning_note(wi, "You are using geometric combination rules in "
4031 "LJ-PME, but your non-bonded C6 parameters do "
4032 "not follow these rules. "
4033 "This will introduce very small errors in the forces and energies in "
4034 "your simulations. If your system is homogeneous, consider using dispersion correction "
4035 "for the total energy and pressure.");
4041 void triple_check(const char *mdparin, t_inputrec *ir, gmx_mtop_t *sys,
4044 char err_buf[STRLEN];
4045 int i, m, c, nmol, npct;
4046 gmx_bool bCharge, bAcc;
4047 real gdt_max, *mgrp, mt;
4049 gmx_mtop_atomloop_block_t aloopb;
4050 gmx_mtop_atomloop_all_t aloop;
4053 char warn_buf[STRLEN];
4055 set_warning_line(wi, mdparin, -1);
4057 if (ir->cutoff_scheme == ecutsVERLET &&
4058 ir->verletbuf_tol > 0 &&
4060 ((EI_MD(ir->eI) || EI_SD(ir->eI)) &&
4061 (ir->etc == etcVRESCALE || ir->etc == etcBERENDSEN)))
4063 /* Check if a too small Verlet buffer might potentially
4064 * cause more drift than the thermostat can couple off.
4066 /* Temperature error fraction for warning and suggestion */
4067 const real T_error_warn = 0.002;
4068 const real T_error_suggest = 0.001;
4069 /* For safety: 2 DOF per atom (typical with constraints) */
4070 const real nrdf_at = 2;
4071 real T, tau, max_T_error;
4076 for (i = 0; i < ir->opts.ngtc; i++)
4078 T = max(T, ir->opts.ref_t[i]);
4079 tau = max(tau, ir->opts.tau_t[i]);
4083 /* This is a worst case estimate of the temperature error,
4084 * assuming perfect buffer estimation and no cancelation
4085 * of errors. The factor 0.5 is because energy distributes
4086 * equally over Ekin and Epot.
4088 max_T_error = 0.5*tau*ir->verletbuf_tol/(nrdf_at*BOLTZ*T);
4089 if (max_T_error > T_error_warn)
4091 sprintf(warn_buf, "With a verlet-buffer-tolerance of %g kJ/mol/ps, a reference temperature of %g and a tau_t of %g, your temperature might be off by up to %.1f%%. To ensure the error is below %.1f%%, decrease verlet-buffer-tolerance to %.0e or decrease tau_t.",
4092 ir->verletbuf_tol, T, tau,
4094 100*T_error_suggest,
4095 ir->verletbuf_tol*T_error_suggest/max_T_error);
4096 warning(wi, warn_buf);
4101 if (ETC_ANDERSEN(ir->etc))
4105 for (i = 0; i < ir->opts.ngtc; i++)
4107 sprintf(err_buf, "all tau_t must currently be equal using Andersen temperature control, violated for group %d", i);
4108 CHECK(ir->opts.tau_t[0] != ir->opts.tau_t[i]);
4109 sprintf(err_buf, "all tau_t must be postive using Andersen temperature control, tau_t[%d]=%10.6f",
4110 i, ir->opts.tau_t[i]);
4111 CHECK(ir->opts.tau_t[i] < 0);
4114 for (i = 0; i < ir->opts.ngtc; i++)
4116 int nsteps = (int)(ir->opts.tau_t[i]/ir->delta_t);
4117 sprintf(err_buf, "tau_t/delta_t for group %d for temperature control method %s must be a multiple of nstcomm (%d), as velocities of atoms in coupled groups are randomized every time step. The input tau_t (%8.3f) leads to %d steps per randomization", i, etcoupl_names[ir->etc], ir->nstcomm, ir->opts.tau_t[i], nsteps);
4118 CHECK((nsteps % ir->nstcomm) && (ir->etc == etcANDERSENMASSIVE));
4122 if (EI_DYNAMICS(ir->eI) && !EI_SD(ir->eI) && ir->eI != eiBD &&
4123 ir->comm_mode == ecmNO &&
4124 !(absolute_reference(ir, sys, FALSE, AbsRef) || ir->nsteps <= 10) &&
4125 !ETC_ANDERSEN(ir->etc))
4127 warning(wi, "You are not using center of mass motion removal (mdp option comm-mode), numerical rounding errors can lead to build up of kinetic energy of the center of mass");
4130 /* Check for pressure coupling with absolute position restraints */
4131 if (ir->epc != epcNO && ir->refcoord_scaling == erscNO)
4133 absolute_reference(ir, sys, TRUE, AbsRef);
4135 for (m = 0; m < DIM; m++)
4137 if (AbsRef[m] && norm2(ir->compress[m]) > 0)
4139 warning(wi, "You are using pressure coupling with absolute position restraints, this will give artifacts. Use the refcoord_scaling option.");
4147 aloopb = gmx_mtop_atomloop_block_init(sys);
4148 while (gmx_mtop_atomloop_block_next(aloopb, &atom, &nmol))
4150 if (atom->q != 0 || atom->qB != 0)
4158 if (EEL_FULL(ir->coulombtype))
4161 "You are using full electrostatics treatment %s for a system without charges.\n"
4162 "This costs a lot of performance for just processing zeros, consider using %s instead.\n",
4163 EELTYPE(ir->coulombtype), EELTYPE(eelCUT));
4164 warning(wi, err_buf);
4169 if (ir->coulombtype == eelCUT && ir->rcoulomb > 0 && !ir->implicit_solvent)
4172 "You are using a plain Coulomb cut-off, which might produce artifacts.\n"
4173 "You might want to consider using %s electrostatics.\n",
4175 warning_note(wi, err_buf);
4179 /* Check if combination rules used in LJ-PME are the same as in the force field */
4180 if (EVDW_PME(ir->vdwtype))
4182 check_combination_rules(ir, sys, wi);
4185 /* Generalized reaction field */
4186 if (ir->opts.ngtc == 0)
4188 sprintf(err_buf, "No temperature coupling while using coulombtype %s",
4190 CHECK(ir->coulombtype == eelGRF);
4194 sprintf(err_buf, "When using coulombtype = %s"
4195 " ref-t for temperature coupling should be > 0",
4197 CHECK((ir->coulombtype == eelGRF) && (ir->opts.ref_t[0] <= 0));
4200 if (ir->eI == eiSD2)
4202 sprintf(warn_buf, "The stochastic dynamics integrator %s is deprecated, since\n"
4203 "it is slower than integrator %s and is slightly less accurate\n"
4204 "with constraints. Use the %s integrator.",
4205 ei_names[ir->eI], ei_names[eiSD1], ei_names[eiSD1]);
4206 warning_note(wi, warn_buf);
4210 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4212 for (m = 0; (m < DIM); m++)
4214 if (fabs(ir->opts.acc[i][m]) > 1e-6)
4223 snew(mgrp, sys->groups.grps[egcACC].nr);
4224 aloop = gmx_mtop_atomloop_all_init(sys);
4225 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
4227 mgrp[ggrpnr(&sys->groups, egcACC, i)] += atom->m;
4230 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4232 for (m = 0; (m < DIM); m++)
4234 acc[m] += ir->opts.acc[i][m]*mgrp[i];
4238 for (m = 0; (m < DIM); m++)
4240 if (fabs(acc[m]) > 1e-6)
4242 const char *dim[DIM] = { "X", "Y", "Z" };
4244 "Net Acceleration in %s direction, will %s be corrected\n",
4245 dim[m], ir->nstcomm != 0 ? "" : "not");
4246 if (ir->nstcomm != 0 && m < ndof_com(ir))
4249 for (i = 0; (i < sys->groups.grps[egcACC].nr); i++)
4251 ir->opts.acc[i][m] -= acc[m];
4259 if (ir->efep != efepNO && ir->fepvals->sc_alpha != 0 &&
4260 !gmx_within_tol(sys->ffparams.reppow, 12.0, 10*GMX_DOUBLE_EPS))
4262 gmx_fatal(FARGS, "Soft-core interactions are only supported with VdW repulsion power 12");
4270 for (i = 0; i < ir->pull->ncoord && !bWarned; i++)
4272 if (ir->pull->coord[i].group[0] == 0 ||
4273 ir->pull->coord[i].group[1] == 0)
4275 absolute_reference(ir, sys, FALSE, AbsRef);
4276 for (m = 0; m < DIM; m++)
4278 if (ir->pull->coord[i].dim[m] && !AbsRef[m])
4280 warning(wi, "You are using an absolute reference for pulling, but the rest of the system does not have an absolute reference. This will lead to artifacts.");
4288 for (i = 0; i < 3; i++)
4290 for (m = 0; m <= i; m++)
4292 if ((ir->epc != epcNO && ir->compress[i][m] != 0) ||
4293 ir->deform[i][m] != 0)
4295 for (c = 0; c < ir->pull->ncoord; c++)
4297 if (ir->pull->coord[c].eGeom == epullgDIRPBC &&
4298 ir->pull->coord[c].vec[m] != 0)
4300 gmx_fatal(FARGS, "Can not have dynamic box while using pull geometry '%s' (dim %c)", EPULLGEOM(ir->pull->coord[c].eGeom), 'x'+m);
4311 void double_check(t_inputrec *ir, matrix box,
4312 gmx_bool bHasNormalConstraints,
4313 gmx_bool bHasAnyConstraints,
4318 char warn_buf[STRLEN];
4321 ptr = check_box(ir->ePBC, box);
4324 warning_error(wi, ptr);
4327 if (bHasNormalConstraints && ir->eConstrAlg == econtSHAKE)
4329 if (ir->shake_tol <= 0.0)
4331 sprintf(warn_buf, "ERROR: shake-tol must be > 0 instead of %g\n",
4333 warning_error(wi, warn_buf);
4336 if (IR_TWINRANGE(*ir) && ir->nstlist > 1)
4338 sprintf(warn_buf, "With twin-range cut-off's and SHAKE the virial and the pressure are incorrect.");
4339 if (ir->epc == epcNO)
4341 warning(wi, warn_buf);
4345 warning_error(wi, warn_buf);
4350 if ( (ir->eConstrAlg == econtLINCS) && bHasNormalConstraints)
4352 /* If we have Lincs constraints: */
4353 if (ir->eI == eiMD && ir->etc == etcNO &&
4354 ir->eConstrAlg == econtLINCS && ir->nLincsIter == 1)
4356 sprintf(warn_buf, "For energy conservation with LINCS, lincs_iter should be 2 or larger.\n");
4357 warning_note(wi, warn_buf);
4360 if ((ir->eI == eiCG || ir->eI == eiLBFGS) && (ir->nProjOrder < 8))
4362 sprintf(warn_buf, "For accurate %s with LINCS constraints, lincs-order should be 8 or more.", ei_names[ir->eI]);
4363 warning_note(wi, warn_buf);
4365 if (ir->epc == epcMTTK)
4367 warning_error(wi, "MTTK not compatible with lincs -- use shake instead.");
4371 if (bHasAnyConstraints && ir->epc == epcMTTK)
4373 warning_error(wi, "Constraints are not implemented with MTTK pressure control.");
4376 if (ir->LincsWarnAngle > 90.0)
4378 sprintf(warn_buf, "lincs-warnangle can not be larger than 90 degrees, setting it to 90.\n");
4379 warning(wi, warn_buf);
4380 ir->LincsWarnAngle = 90.0;
4383 if (ir->ePBC != epbcNONE)
4385 if (ir->nstlist == 0)
4387 warning(wi, "With nstlist=0 atoms are only put into the box at step 0, therefore drifting atoms might cause the simulation to crash.");
4389 bTWIN = (ir->rlistlong > ir->rlist);
4390 if (ir->ns_type == ensGRID)
4392 if (sqr(ir->rlistlong) >= max_cutoff2(ir->ePBC, box))
4394 sprintf(warn_buf, "ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease %s.\n",
4395 bTWIN ? (ir->rcoulomb == ir->rlistlong ? "rcoulomb" : "rvdw") : "rlist");
4396 warning_error(wi, warn_buf);
4401 min_size = min(box[XX][XX], min(box[YY][YY], box[ZZ][ZZ]));
4402 if (2*ir->rlistlong >= min_size)
4404 sprintf(warn_buf, "ERROR: One of the box lengths is smaller than twice the cut-off length. Increase the box size or decrease rlist.");
4405 warning_error(wi, warn_buf);
4408 fprintf(stderr, "Grid search might allow larger cut-off's than simple search with triclinic boxes.");
4415 void check_chargegroup_radii(const gmx_mtop_t *mtop, const t_inputrec *ir,
4419 real rvdw1, rvdw2, rcoul1, rcoul2;
4420 char warn_buf[STRLEN];
4422 calc_chargegroup_radii(mtop, x, &rvdw1, &rvdw2, &rcoul1, &rcoul2);
4426 printf("Largest charge group radii for Van der Waals: %5.3f, %5.3f nm\n",
4431 printf("Largest charge group radii for Coulomb: %5.3f, %5.3f nm\n",
4437 if (rvdw1 + rvdw2 > ir->rlist ||
4438 rcoul1 + rcoul2 > ir->rlist)
4441 "The sum of the two largest charge group radii (%f) "
4442 "is larger than rlist (%f)\n",
4443 max(rvdw1+rvdw2, rcoul1+rcoul2), ir->rlist);
4444 warning(wi, warn_buf);
4448 /* Here we do not use the zero at cut-off macro,
4449 * since user defined interactions might purposely
4450 * not be zero at the cut-off.
4452 if (ir_vdw_is_zero_at_cutoff(ir) &&
4453 rvdw1 + rvdw2 > ir->rlistlong - ir->rvdw)
4455 sprintf(warn_buf, "The sum of the two largest charge group "
4456 "radii (%f) is larger than %s (%f) - rvdw (%f).\n"
4457 "With exact cut-offs, better performance can be "
4458 "obtained with cutoff-scheme = %s, because it "
4459 "does not use charge groups at all.",
4461 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4462 ir->rlistlong, ir->rvdw,
4463 ecutscheme_names[ecutsVERLET]);
4466 warning(wi, warn_buf);
4470 warning_note(wi, warn_buf);
4473 if (ir_coulomb_is_zero_at_cutoff(ir) &&
4474 rcoul1 + rcoul2 > ir->rlistlong - ir->rcoulomb)
4476 sprintf(warn_buf, "The sum of the two largest charge group radii (%f) is larger than %s (%f) - rcoulomb (%f).\n"
4477 "With exact cut-offs, better performance can be obtained with cutoff-scheme = %s, because it does not use charge groups at all.",
4479 ir->rlistlong > ir->rlist ? "rlistlong" : "rlist",
4480 ir->rlistlong, ir->rcoulomb,
4481 ecutscheme_names[ecutsVERLET]);
4484 warning(wi, warn_buf);
4488 warning_note(wi, warn_buf);